<?xml version="1.0" encoding="UTF-8"?>
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            <method name="HermesDataDiffExpr" signature="" line-rate="1" branch-rate="0" complexity="0">
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                <line number="294" hits="2" branch="false"/>
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              <lines>
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        </class>
        <class name="draw_heatmap.R" filename="R/draw_heatmap.R" line-rate="0.971428571428571" branch-rate="0" complexity="0">
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                <line number="43" hits="1" branch="false"/>
                <line number="44" hits="1" branch="false"/>
                <line number="45" hits="1" branch="false"/>
                <line number="46" hits="1" branch="false"/>
                <line number="47" hits="1" branch="false"/>
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                <line number="56" hits="1" branch="false"/>
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                <line number="78" hits="1" branch="false"/>
                <line number="79" hits="1" branch="false"/>
                <line number="80" hits="1" branch="false"/>
                <line number="81" hits="1" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="42" hits="1" branch="false"/>
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            <line number="81" hits="1" branch="false"/>
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        </class>
        <class name="draw_scatterplot.R" filename="R/draw_scatterplot.R" line-rate="0.875" branch-rate="0" complexity="0">
          <methods>
            <method name="draw_scatterplot" signature="" line-rate="0.875" branch-rate="0" complexity="0">
              <lines>
                <line number="56" hits="1" branch="false"/>
                <line number="57" hits="1" branch="false"/>
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                <line number="92" hits="1" branch="false"/>
                <line number="93" hits="0" branch="false"/>
                <line number="95" hits="1" branch="false"/>
              </lines>
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            <line number="95" hits="1" branch="false"/>
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        </class>
        <class name="GeneSpec-class.R" filename="R/GeneSpec-class.R" line-rate="1" branch-rate="0" complexity="0">
          <methods>
            <method name="h_unique_labels" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="18" hits="47" branch="false"/>
                <line number="19" hits="5" branch="false"/>
                <line number="21" hits="42" branch="false"/>
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                <line number="23" hits="15" branch="false"/>
                <line number="25" hits="27" branch="false"/>
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                <line number="31" hits="8" branch="false"/>
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                <line number="33" hits="8" branch="false"/>
                <line number="34" hits="8" branch="false"/>
                <line number="36" hits="27" branch="false"/>
                <line number="37" hits="27" branch="false"/>
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            </method>
            <method name="initialize" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="92" hits="41" branch="false"/>
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                <line number="95" hits="41" branch="false"/>
                <line number="96" hits="41" branch="false"/>
                <line number="97" hits="41" branch="false"/>
              </lines>
            </method>
            <method name="get_genes" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="101" hits="29" branch="false"/>
              </lines>
            </method>
            <method name="get_gene_labels" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="107" hits="26" branch="false"/>
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            </method>
            <method name="returns_vector" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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            </method>
            <method name="get_label" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="121" hits="4" branch="false"/>
                <line number="123" hits="2" branch="false"/>
                <line number="126" hits="8" branch="false"/>
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            </method>
            <method name="extract" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="137" hits="23" branch="false"/>
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                <line number="140" hits="7" branch="false"/>
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                <line number="148" hits="13" branch="false"/>
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                <line number="151" hits="10" branch="false"/>
              </lines>
            </method>
            <method name="extract_data_frame" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="170" hits="10" branch="false"/>
                <line number="171" hits="10" branch="false"/>
                <line number="172" hits="10" branch="false"/>
              </lines>
            </method>
            <method name="gene_spec" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="206" hits="9" branch="false"/>
                <line number="207" hits="9" branch="false"/>
                <line number="208" hits="9" branch="false"/>
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                <line number="210" hits="9" branch="false"/>
              </lines>
            </method>
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            <line number="208" hits="9" branch="false"/>
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            <line number="210" hits="9" branch="false"/>
          </lines>
        </class>
        <class name="graphs.R" filename="R/graphs.R" line-rate="0.97196261682243" branch-rate="0" complexity="0">
          <methods>
            <method name="draw_libsize_hist" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="20" hits="3" branch="false"/>
                <line number="21" hits="3" branch="false"/>
                <line number="22" hits="3" branch="false"/>
                <line number="23" hits="3" branch="false"/>
                <line number="24" hits="3" branch="false"/>
                <line number="25" hits="3" branch="false"/>
                <line number="26" hits="3" branch="false"/>
                <line number="27" hits="3" branch="false"/>
                <line number="28" hits="3" branch="false"/>
                <line number="29" hits="3" branch="false"/>
                <line number="30" hits="3" branch="false"/>
                <line number="31" hits="3" branch="false"/>
                <line number="32" hits="3" branch="false"/>
                <line number="33" hits="3" branch="false"/>
                <line number="34" hits="3" branch="false"/>
                <line number="35" hits="3" branch="false"/>
                <line number="36" hits="3" branch="false"/>
              </lines>
            </method>
            <method name="draw_libsize_qq" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="62" hits="3" branch="false"/>
                <line number="63" hits="3" branch="false"/>
                <line number="64" hits="3" branch="false"/>
                <line number="65" hits="3" branch="false"/>
                <line number="66" hits="3" branch="false"/>
                <line number="67" hits="3" branch="false"/>
                <line number="68" hits="3" branch="false"/>
                <line number="69" hits="3" branch="false"/>
                <line number="70" hits="3" branch="false"/>
                <line number="71" hits="3" branch="false"/>
                <line number="72" hits="3" branch="false"/>
                <line number="73" hits="3" branch="false"/>
                <line number="74" hits="3" branch="false"/>
                <line number="75" hits="3" branch="false"/>
                <line number="76" hits="3" branch="false"/>
              </lines>
            </method>
            <method name="draw_libsize_densities" signature="" line-rate="0.842105263157895" branch-rate="0" complexity="0">
              <lines>
                <line number="97" hits="3" branch="false"/>
                <line number="98" hits="3" branch="false"/>
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                <line number="101" hits="3" branch="false"/>
                <line number="102" hits="3" branch="false"/>
                <line number="103" hits="3" branch="false"/>
                <line number="104" hits="3" branch="false"/>
                <line number="105" hits="3" branch="false"/>
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                <line number="109" hits="0" branch="false"/>
                <line number="111" hits="3" branch="false"/>
                <line number="112" hits="3" branch="false"/>
                <line number="113" hits="3" branch="false"/>
                <line number="114" hits="3" branch="false"/>
                <line number="115" hits="3" branch="false"/>
                <line number="116" hits="3" branch="false"/>
                <line number="117" hits="3" branch="false"/>
              </lines>
            </method>
            <method name="draw_nonzero_boxplot" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="148" hits="4" branch="false"/>
                <line number="149" hits="4" branch="false"/>
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                <line number="151" hits="4" branch="false"/>
                <line number="152" hits="4" branch="false"/>
                <line number="154" hits="4" branch="false"/>
                <line number="155" hits="4" branch="false"/>
                <line number="157" hits="4" branch="false"/>
                <line number="158" hits="4" branch="false"/>
                <line number="159" hits="4" branch="false"/>
                <line number="160" hits="4" branch="false"/>
                <line number="161" hits="4" branch="false"/>
                <line number="162" hits="4" branch="false"/>
                <line number="163" hits="4" branch="false"/>
                <line number="164" hits="4" branch="false"/>
                <line number="165" hits="4" branch="false"/>
                <line number="166" hits="4" branch="false"/>
                <line number="167" hits="4" branch="false"/>
              </lines>
            </method>
            <method name="draw_genes_barplot" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="200" hits="4" branch="false"/>
                <line number="201" hits="4" branch="false"/>
                <line number="202" hits="4" branch="false"/>
                <line number="203" hits="4" branch="false"/>
                <line number="204" hits="4" branch="false"/>
                <line number="205" hits="4" branch="false"/>
                <line number="206" hits="4" branch="false"/>
                <line number="208" hits="4" branch="false"/>
                <line number="209" hits="4" branch="false"/>
                <line number="210" hits="4" branch="false"/>
                <line number="211" hits="4" branch="false"/>
                <line number="212" hits="4" branch="false"/>
                <line number="214" hits="4" branch="false"/>
                <line number="215" hits="4" branch="false"/>
                <line number="216" hits="4" branch="false"/>
                <line number="217" hits="4" branch="false"/>
                <line number="219" hits="1" branch="false"/>
                <line number="221" hits="4" branch="false"/>
                <line number="222" hits="4" branch="false"/>
                <line number="223" hits="4" branch="false"/>
                <line number="224" hits="4" branch="false"/>
                <line number="225" hits="4" branch="false"/>
                <line number="226" hits="4" branch="false"/>
              </lines>
            </method>
            <method name="AnyHermesData" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="44" hits="8" branch="false"/>
                <line number="45" hits="7" branch="false"/>
                <line number="46" hits="7" branch="false"/>
                <line number="48" hits="6" branch="false"/>
                <line number="49" hits="6" branch="false"/>
                <line number="50" hits="6" branch="false"/>
                <line number="51" hits="6" branch="false"/>
                <line number="256" hits="2" branch="false"/>
                <line number="257" hits="2" branch="false"/>
                <line number="258" hits="2" branch="false"/>
                <line number="259" hits="2" branch="false"/>
                <line number="260" hits="2" branch="false"/>
                <line number="261" hits="2" branch="false"/>
                <line number="262" hits="2" branch="false"/>
                <line number="263" hits="2" branch="false"/>
                <line number="264" hits="2" branch="false"/>
                <line number="265" hits="2" branch="false"/>
                <line number="266" hits="2" branch="false"/>
                <line number="267" hits="2" branch="false"/>
                <line number="268" hits="2" branch="false"/>
                <line number="269" hits="2" branch="false"/>
                <line number="270" hits="2" branch="false"/>
                <line number="126" hits="15" branch="false"/>
                <line number="207" hits="123" branch="false"/>
                <line number="282" hits="4" branch="false"/>
                <line number="313" hits="4" branch="false"/>
                <line number="440" hits="9" branch="false"/>
                <line number="441" hits="9" branch="false"/>
                <line number="442" hits="9" branch="false"/>
                <line number="443" hits="9" branch="false"/>
                <line number="444" hits="9" branch="false"/>
                <line number="445" hits="9" branch="false"/>
                <line number="446" hits="9" branch="false"/>
                <line number="447" hits="9" branch="false"/>
                <line number="448" hits="9" branch="false"/>
                <line number="449" hits="9" branch="false"/>
                <line number="450" hits="8" branch="false"/>
                <line number="451" hits="7" branch="false"/>
                <line number="452" hits="8" branch="false"/>
                <line number="453" hits="1" branch="false"/>
                <line number="454" hits="8" branch="false"/>
                <line number="455" hits="8" branch="false"/>
                <line number="456" hits="7" branch="false"/>
                <line number="457" hits="8" branch="false"/>
                <line number="458" hits="1" branch="false"/>
                <line number="459" hits="8" branch="false"/>
                <line number="460" hits="8" branch="false"/>
                <line number="461" hits="1" branch="false"/>
                <line number="463" hits="8" branch="false"/>
                <line number="464" hits="1" branch="false"/>
                <line number="466" hits="8" branch="false"/>
                <line number="504" hits="6" branch="false"/>
                <line number="505" hits="6" branch="false"/>
                <line number="506" hits="6" branch="false"/>
                <line number="524" hits="6" branch="false"/>
                <line number="525" hits="6" branch="false"/>
                <line number="526" hits="6" branch="false"/>
                <line number="682" hits="4" branch="false"/>
                <line number="683" hits="4" branch="false"/>
                <line number="685" hits="4" branch="false"/>
                <line number="686" hits="4" branch="false"/>
                <line number="687" hits="4" branch="false"/>
                <line number="689" hits="4" branch="false"/>
                <line number="690" hits="4" branch="false"/>
                <line number="691" hits="4" branch="false"/>
                <line number="692" hits="4" branch="false"/>
                <line number="694" hits="4" branch="false"/>
                <line number="695" hits="4" branch="false"/>
                <line number="696" hits="4" branch="false"/>
                <line number="697" hits="4" branch="false"/>
                <line number="698" hits="4" branch="false"/>
                <line number="699" hits="4" branch="false"/>
                <line number="700" hits="4" branch="false"/>
                <line number="701" hits="4" branch="false"/>
                <line number="702" hits="4" branch="false"/>
                <line number="703" hits="4" branch="false"/>
                <line number="704" hits="4" branch="false"/>
                <line number="705" hits="4" branch="false"/>
                <line number="107" hits="16" branch="false"/>
                <line number="108" hits="16" branch="false"/>
                <line number="109" hits="16" branch="false"/>
                <line number="110" hits="16" branch="false"/>
                <line number="111" hits="16" branch="false"/>
                <line number="112" hits="16" branch="false"/>
                <line number="113" hits="16" branch="false"/>
                <line number="114" hits="16" branch="false"/>
                <line number="115" hits="16" branch="false"/>
                <line number="116" hits="16" branch="false"/>
                <line number="117" hits="14" branch="false"/>
                <line number="119" hits="14" branch="false"/>
                <line number="120" hits="59" branch="false"/>
                <line number="121" hits="59" branch="false"/>
                <line number="122" hits="59" branch="false"/>
                <line number="123" hits="59" branch="false"/>
                <line number="124" hits="59" branch="false"/>
                <line number="125" hits="58" branch="false"/>
                <line number="127" hits="13" branch="false"/>
                <line number="128" hits="13" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="20" hits="3" branch="false"/>
            <line number="21" hits="3" branch="false"/>
            <line number="22" hits="3" branch="false"/>
            <line number="23" hits="3" branch="false"/>
            <line number="24" hits="3" branch="false"/>
            <line number="25" hits="3" branch="false"/>
            <line number="26" hits="3" branch="false"/>
            <line number="27" hits="3" branch="false"/>
            <line number="28" hits="3" branch="false"/>
            <line number="29" hits="3" branch="false"/>
            <line number="30" hits="3" branch="false"/>
            <line number="31" hits="3" branch="false"/>
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            <line number="33" hits="3" branch="false"/>
            <line number="34" hits="3" branch="false"/>
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            <line number="69" hits="3" branch="false"/>
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            <line number="71" hits="3" branch="false"/>
            <line number="72" hits="3" branch="false"/>
            <line number="73" hits="3" branch="false"/>
            <line number="74" hits="3" branch="false"/>
            <line number="75" hits="3" branch="false"/>
            <line number="76" hits="3" branch="false"/>
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            <line number="99" hits="3" branch="false"/>
            <line number="100" hits="3" branch="false"/>
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            <line number="102" hits="3" branch="false"/>
            <line number="103" hits="3" branch="false"/>
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            <line number="112" hits="3" branch="false"/>
            <line number="113" hits="3" branch="false"/>
            <line number="114" hits="3" branch="false"/>
            <line number="115" hits="3" branch="false"/>
            <line number="116" hits="3" branch="false"/>
            <line number="117" hits="3" branch="false"/>
            <line number="148" hits="4" branch="false"/>
            <line number="149" hits="4" branch="false"/>
            <line number="150" hits="4" branch="false"/>
            <line number="151" hits="4" branch="false"/>
            <line number="152" hits="4" branch="false"/>
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            <line number="157" hits="4" branch="false"/>
            <line number="158" hits="4" branch="false"/>
            <line number="159" hits="4" branch="false"/>
            <line number="160" hits="4" branch="false"/>
            <line number="161" hits="4" branch="false"/>
            <line number="162" hits="4" branch="false"/>
            <line number="163" hits="4" branch="false"/>
            <line number="164" hits="4" branch="false"/>
            <line number="165" hits="4" branch="false"/>
            <line number="166" hits="4" branch="false"/>
            <line number="167" hits="4" branch="false"/>
            <line number="200" hits="4" branch="false"/>
            <line number="201" hits="4" branch="false"/>
            <line number="202" hits="4" branch="false"/>
            <line number="203" hits="4" branch="false"/>
            <line number="204" hits="4" branch="false"/>
            <line number="205" hits="4" branch="false"/>
            <line number="206" hits="4" branch="false"/>
            <line number="208" hits="4" branch="false"/>
            <line number="209" hits="4" branch="false"/>
            <line number="210" hits="4" branch="false"/>
            <line number="211" hits="4" branch="false"/>
            <line number="212" hits="4" branch="false"/>
            <line number="214" hits="4" branch="false"/>
            <line number="215" hits="4" branch="false"/>
            <line number="216" hits="4" branch="false"/>
            <line number="217" hits="4" branch="false"/>
            <line number="219" hits="1" branch="false"/>
            <line number="221" hits="4" branch="false"/>
            <line number="222" hits="4" branch="false"/>
            <line number="223" hits="4" branch="false"/>
            <line number="224" hits="4" branch="false"/>
            <line number="225" hits="4" branch="false"/>
            <line number="226" hits="4" branch="false"/>
            <line number="256" hits="2" branch="false"/>
            <line number="257" hits="2" branch="false"/>
            <line number="258" hits="2" branch="false"/>
            <line number="259" hits="2" branch="false"/>
            <line number="260" hits="2" branch="false"/>
            <line number="261" hits="2" branch="false"/>
            <line number="262" hits="2" branch="false"/>
            <line number="263" hits="2" branch="false"/>
            <line number="264" hits="2" branch="false"/>
            <line number="265" hits="2" branch="false"/>
            <line number="266" hits="2" branch="false"/>
            <line number="267" hits="2" branch="false"/>
            <line number="268" hits="2" branch="false"/>
            <line number="269" hits="2" branch="false"/>
            <line number="270" hits="2" branch="false"/>
          </lines>
        </class>
        <class name="HermesData-class.R" filename="R/HermesData-class.R" line-rate="0.885714285714286" branch-rate="0" complexity="0">
          <methods>
            <method name="HermesData" signature="" line-rate="0.862068965517241" branch-rate="0" complexity="0">
              <lines>
                <line number="109" hits="80" branch="false"/>
                <line number="110" hits="80" branch="false"/>
                <line number="111" hits="80" branch="false"/>
                <line number="112" hits="80" branch="false"/>
                <line number="114" hits="79" branch="false"/>
                <line number="115" hits="79" branch="false"/>
                <line number="116" hits="1" branch="false"/>
                <line number="117" hits="1" branch="false"/>
                <line number="118" hits="79" branch="false"/>
                <line number="119" hits="79" branch="false"/>
                <line number="120" hits="79" branch="false"/>
                <line number="122" hits="79" branch="false"/>
                <line number="123" hits="79" branch="false"/>
                <line number="125" hits="79" branch="false"/>
                <line number="126" hits="79" branch="false"/>
                <line number="128" hits="79" branch="false"/>
                <line number="129" hits="79" branch="false"/>
                <line number="130" hits="14" branch="false"/>
                <line number="131" hits="79" branch="false"/>
                <line number="132" hits="65" branch="false"/>
                <line number="133" hits="79" branch="false"/>
                <line number="134" hits="0" branch="false"/>
                <line number="135" hits="0" branch="false"/>
                <line number="136" hits="0" branch="false"/>
                <line number="137" hits="0" branch="false"/>
                <line number="138" hits="79" branch="false"/>
                <line number="140" hits="79" branch="false"/>
                <line number="141" hits="14" branch="false"/>
                <line number="143" hits="65" branch="false"/>
              </lines>
            </method>
            <method name="HermesDataFromMatrix" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="159" hits="3" branch="false"/>
                <line number="163" hits="3" branch="false"/>
                <line number="164" hits="3" branch="false"/>
                <line number="165" hits="3" branch="false"/>
                <line number="166" hits="3" branch="false"/>
                <line number="167" hits="3" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="109" hits="80" branch="false"/>
            <line number="110" hits="80" branch="false"/>
            <line number="111" hits="80" branch="false"/>
            <line number="112" hits="80" branch="false"/>
            <line number="114" hits="79" branch="false"/>
            <line number="115" hits="79" branch="false"/>
            <line number="116" hits="1" branch="false"/>
            <line number="117" hits="1" branch="false"/>
            <line number="118" hits="79" branch="false"/>
            <line number="119" hits="79" branch="false"/>
            <line number="120" hits="79" branch="false"/>
            <line number="122" hits="79" branch="false"/>
            <line number="123" hits="79" branch="false"/>
            <line number="125" hits="79" branch="false"/>
            <line number="126" hits="79" branch="false"/>
            <line number="128" hits="79" branch="false"/>
            <line number="129" hits="79" branch="false"/>
            <line number="130" hits="14" branch="false"/>
            <line number="131" hits="79" branch="false"/>
            <line number="132" hits="65" branch="false"/>
            <line number="133" hits="79" branch="false"/>
            <line number="134" hits="0" branch="false"/>
            <line number="135" hits="0" branch="false"/>
            <line number="136" hits="0" branch="false"/>
            <line number="137" hits="0" branch="false"/>
            <line number="138" hits="79" branch="false"/>
            <line number="140" hits="79" branch="false"/>
            <line number="141" hits="14" branch="false"/>
            <line number="143" hits="65" branch="false"/>
            <line number="159" hits="3" branch="false"/>
            <line number="163" hits="3" branch="false"/>
            <line number="164" hits="3" branch="false"/>
            <line number="165" hits="3" branch="false"/>
            <line number="166" hits="3" branch="false"/>
            <line number="167" hits="3" branch="false"/>
          </lines>
        </class>
        <class name="HermesData-methods.R" filename="R/HermesData-methods.R" line-rate="1" branch-rate="0" complexity="0">
          <methods>
            <method name="AnyHermesData" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="44" hits="8" branch="false"/>
                <line number="45" hits="7" branch="false"/>
                <line number="46" hits="7" branch="false"/>
                <line number="48" hits="6" branch="false"/>
                <line number="49" hits="6" branch="false"/>
                <line number="50" hits="6" branch="false"/>
                <line number="51" hits="6" branch="false"/>
                <line number="256" hits="2" branch="false"/>
                <line number="257" hits="2" branch="false"/>
                <line number="258" hits="2" branch="false"/>
                <line number="259" hits="2" branch="false"/>
                <line number="260" hits="2" branch="false"/>
                <line number="261" hits="2" branch="false"/>
                <line number="262" hits="2" branch="false"/>
                <line number="263" hits="2" branch="false"/>
                <line number="264" hits="2" branch="false"/>
                <line number="265" hits="2" branch="false"/>
                <line number="266" hits="2" branch="false"/>
                <line number="267" hits="2" branch="false"/>
                <line number="268" hits="2" branch="false"/>
                <line number="269" hits="2" branch="false"/>
                <line number="270" hits="2" branch="false"/>
                <line number="126" hits="15" branch="false"/>
                <line number="207" hits="123" branch="false"/>
                <line number="282" hits="4" branch="false"/>
                <line number="313" hits="4" branch="false"/>
                <line number="440" hits="9" branch="false"/>
                <line number="441" hits="9" branch="false"/>
                <line number="442" hits="9" branch="false"/>
                <line number="443" hits="9" branch="false"/>
                <line number="444" hits="9" branch="false"/>
                <line number="445" hits="9" branch="false"/>
                <line number="446" hits="9" branch="false"/>
                <line number="447" hits="9" branch="false"/>
                <line number="448" hits="9" branch="false"/>
                <line number="449" hits="9" branch="false"/>
                <line number="450" hits="8" branch="false"/>
                <line number="451" hits="7" branch="false"/>
                <line number="452" hits="8" branch="false"/>
                <line number="453" hits="1" branch="false"/>
                <line number="454" hits="8" branch="false"/>
                <line number="455" hits="8" branch="false"/>
                <line number="456" hits="7" branch="false"/>
                <line number="457" hits="8" branch="false"/>
                <line number="458" hits="1" branch="false"/>
                <line number="459" hits="8" branch="false"/>
                <line number="460" hits="8" branch="false"/>
                <line number="461" hits="1" branch="false"/>
                <line number="463" hits="8" branch="false"/>
                <line number="464" hits="1" branch="false"/>
                <line number="466" hits="8" branch="false"/>
                <line number="504" hits="6" branch="false"/>
                <line number="505" hits="6" branch="false"/>
                <line number="506" hits="6" branch="false"/>
                <line number="524" hits="6" branch="false"/>
                <line number="525" hits="6" branch="false"/>
                <line number="526" hits="6" branch="false"/>
                <line number="682" hits="4" branch="false"/>
                <line number="683" hits="4" branch="false"/>
                <line number="685" hits="4" branch="false"/>
                <line number="686" hits="4" branch="false"/>
                <line number="687" hits="4" branch="false"/>
                <line number="689" hits="4" branch="false"/>
                <line number="690" hits="4" branch="false"/>
                <line number="691" hits="4" branch="false"/>
                <line number="692" hits="4" branch="false"/>
                <line number="694" hits="4" branch="false"/>
                <line number="695" hits="4" branch="false"/>
                <line number="696" hits="4" branch="false"/>
                <line number="697" hits="4" branch="false"/>
                <line number="698" hits="4" branch="false"/>
                <line number="699" hits="4" branch="false"/>
                <line number="700" hits="4" branch="false"/>
                <line number="701" hits="4" branch="false"/>
                <line number="702" hits="4" branch="false"/>
                <line number="703" hits="4" branch="false"/>
                <line number="704" hits="4" branch="false"/>
                <line number="705" hits="4" branch="false"/>
                <line number="107" hits="16" branch="false"/>
                <line number="108" hits="16" branch="false"/>
                <line number="109" hits="16" branch="false"/>
                <line number="110" hits="16" branch="false"/>
                <line number="111" hits="16" branch="false"/>
                <line number="112" hits="16" branch="false"/>
                <line number="113" hits="16" branch="false"/>
                <line number="114" hits="16" branch="false"/>
                <line number="115" hits="16" branch="false"/>
                <line number="116" hits="16" branch="false"/>
                <line number="117" hits="14" branch="false"/>
                <line number="119" hits="14" branch="false"/>
                <line number="120" hits="59" branch="false"/>
                <line number="121" hits="59" branch="false"/>
                <line number="122" hits="59" branch="false"/>
                <line number="123" hits="59" branch="false"/>
                <line number="124" hits="59" branch="false"/>
                <line number="125" hits="58" branch="false"/>
                <line number="127" hits="13" branch="false"/>
                <line number="128" hits="13" branch="false"/>
              </lines>
            </method>
            <method name="AnyHermesData#DataFrame" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="156" hits="3" branch="false"/>
                <line number="157" hits="3" branch="false"/>
                <line number="158" hits="3" branch="false"/>
                <line number="159" hits="3" branch="false"/>
                <line number="160" hits="3" branch="false"/>
                <line number="161" hits="3" branch="false"/>
                <line number="162" hits="1" branch="false"/>
                <line number="163" hits="1" branch="false"/>
                <line number="164" hits="1" branch="false"/>
                <line number="165" hits="1" branch="false"/>
                <line number="166" hits="1" branch="false"/>
                <line number="168" hits="3" branch="false"/>
                <line number="169" hits="3" branch="false"/>
                <line number="170" hits="3" branch="false"/>
                <line number="171" hits="1" branch="false"/>
                <line number="173" hits="3" branch="false"/>
                <line number="174" hits="3" branch="false"/>
              </lines>
            </method>
            <method name="AnyHermesData#matrix" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="228" hits="1" branch="false"/>
                <line number="229" hits="1" branch="false"/>
                <line number="230" hits="1" branch="false"/>
              </lines>
            </method>
            <method name="ANY" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="252" hits="1" branch="false"/>
              </lines>
            </method>
            <method name="genes" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="271" hits="4" branch="false"/>
              </lines>
            </method>
            <method name="filter" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="366" hits="10" branch="false"/>
              </lines>
            </method>
            <method name="h_has_req_annotations" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="392" hits="9" branch="false"/>
                <line number="393" hits="9" branch="false"/>
                <line number="394" hits="9" branch="false"/>
                <line number="395" hits="9" branch="false"/>
                <line number="396" hits="9" branch="false"/>
                <line number="397" hits="9" branch="false"/>
              </lines>
            </method>
            <method name="extraColDataNames" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="494" hits="6" branch="false"/>
              </lines>
            </method>
            <method name="extraRowDataNames" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="514" hits="6" branch="false"/>
              </lines>
            </method>
            <method name="h_map_pos" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="547" hits="7" branch="false"/>
                <line number="548" hits="7" branch="false"/>
                <line number="549" hits="7" branch="false"/>
                <line number="550" hits="7" branch="false"/>
                <line number="551" hits="7" branch="false"/>
                <line number="552" hits="7" branch="false"/>
                <line number="553" hits="7" branch="false"/>
                <line number="554" hits="7" branch="false"/>
                <line number="555" hits="7" branch="false"/>
                <line number="556" hits="7" branch="false"/>
                <line number="557" hits="7" branch="false"/>
                <line number="558" hits="7" branch="false"/>
                <line number="559" hits="7" branch="false"/>
                <line number="560" hits="6" branch="false"/>
              </lines>
            </method>
            <method name="SummarizedExperiment" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="611" hits="5" branch="false"/>
                <line number="612" hits="1" branch="false"/>
                <line number="613" hits="1" branch="false"/>
                <line number="614" hits="1" branch="false"/>
                <line number="616" hits="5" branch="false"/>
                <line number="617" hits="1" branch="false"/>
                <line number="618" hits="1" branch="false"/>
                <line number="619" hits="1" branch="false"/>
                <line number="621" hits="5" branch="false"/>
                <line number="622" hits="3" branch="false"/>
                <line number="623" hits="3" branch="false"/>
                <line number="624" hits="3" branch="false"/>
                <line number="626" hits="5" branch="false"/>
                <line number="937" hits="5" branch="false"/>
                <line number="938" hits="5" branch="false"/>
              </lines>
            </method>
            <method name="HermesDataSummary" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="725" hits="2" branch="false"/>
                <line number="726" hits="2" branch="false"/>
                <line number="727" hits="2" branch="false"/>
                <line number="728" hits="2" branch="false"/>
                <line number="729" hits="2" branch="false"/>
                <line number="730" hits="2" branch="false"/>
                <line number="731" hits="2" branch="false"/>
                <line number="732" hits="2" branch="false"/>
                <line number="733" hits="2" branch="false"/>
                <line number="734" hits="2" branch="false"/>
                <line number="735" hits="2" branch="false"/>
                <line number="736" hits="2" branch="false"/>
                <line number="737" hits="2" branch="false"/>
                <line number="738" hits="2" branch="false"/>
                <line number="739" hits="2" branch="false"/>
                <line number="740" hits="2" branch="false"/>
                <line number="741" hits="1" branch="false"/>
                <line number="742" hits="1" branch="false"/>
                <line number="743" hits="1" branch="false"/>
                <line number="744" hits="1" branch="false"/>
                <line number="746" hits="2" branch="false"/>
                <line number="747" hits="1" branch="false"/>
                <line number="748" hits="1" branch="false"/>
                <line number="749" hits="1" branch="false"/>
                <line number="750" hits="1" branch="false"/>
                <line number="752" hits="2" branch="false"/>
                <line number="753" hits="1" branch="false"/>
                <line number="754" hits="1" branch="false"/>
                <line number="755" hits="1" branch="false"/>
                <line number="757" hits="1" branch="false"/>
                <line number="758" hits="1" branch="false"/>
                <line number="759" hits="1" branch="false"/>
                <line number="760" hits="1" branch="false"/>
                <line number="761" hits="1" branch="false"/>
                <line number="762" hits="1" branch="false"/>
                <line number="763" hits="1" branch="false"/>
                <line number="764" hits="1" branch="false"/>
              </lines>
            </method>
            <method name=".show.AnyHermesData" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="772" hits="2" branch="false"/>
                <line number="773" hits="2" branch="false"/>
                <line number="774" hits="2" branch="false"/>
                <line number="775" hits="2" branch="false"/>
                <line number="776" hits="2" branch="false"/>
                <line number="777" hits="2" branch="false"/>
                <line number="778" hits="2" branch="false"/>
                <line number="779" hits="2" branch="false"/>
                <line number="780" hits="2" branch="false"/>
                <line number="781" hits="2" branch="false"/>
                <line number="782" hits="2" branch="false"/>
                <line number="783" hits="2" branch="false"/>
                <line number="784" hits="2" branch="false"/>
                <line number="785" hits="2" branch="false"/>
                <line number="786" hits="2" branch="false"/>
                <line number="787" hits="2" branch="false"/>
                <line number="788" hits="2" branch="false"/>
                <line number="789" hits="2" branch="false"/>
                <line number="790" hits="2" branch="false"/>
                <line number="791" hits="2" branch="false"/>
                <line number="792" hits="2" branch="false"/>
                <line number="793" hits="2" branch="false"/>
                <line number="794" hits="2" branch="false"/>
                <line number="795" hits="2" branch="false"/>
              </lines>
            </method>
            <method name="correlate" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="854" hits="14" branch="false"/>
              </lines>
            </method>
            <method name="MultiAssayExperiment" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="891" hits="3" branch="false"/>
                <line number="892" hits="3" branch="false"/>
                <line number="893" hits="3" branch="false"/>
                <line number="894" hits="2" branch="false"/>
                <line number="895" hits="3" branch="false"/>
                <line number="896" hits="1" branch="false"/>
                <line number="897" hits="3" branch="false"/>
                <line number="898" hits="3" branch="false"/>
                <line number="899" hits="2" branch="false"/>
                <line number="900" hits="2" branch="false"/>
                <line number="901" hits="1" branch="false"/>
                <line number="902" hits="1" branch="false"/>
                <line number="903" hits="1" branch="false"/>
                <line number="904" hits="1" branch="false"/>
                <line number="906" hits="2" branch="false"/>
                <line number="907" hits="2" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="126" hits="15" branch="false"/>
            <line number="156" hits="3" branch="false"/>
            <line number="157" hits="3" branch="false"/>
            <line number="158" hits="3" branch="false"/>
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            <line number="160" hits="3" branch="false"/>
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            <line number="162" hits="1" branch="false"/>
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            <line number="164" hits="1" branch="false"/>
            <line number="165" hits="1" branch="false"/>
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            <line number="168" hits="3" branch="false"/>
            <line number="169" hits="3" branch="false"/>
            <line number="170" hits="3" branch="false"/>
            <line number="171" hits="1" branch="false"/>
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            <line number="728" hits="2" branch="false"/>
            <line number="729" hits="2" branch="false"/>
            <line number="730" hits="2" branch="false"/>
            <line number="731" hits="2" branch="false"/>
            <line number="732" hits="2" branch="false"/>
            <line number="733" hits="2" branch="false"/>
            <line number="734" hits="2" branch="false"/>
            <line number="735" hits="2" branch="false"/>
            <line number="736" hits="2" branch="false"/>
            <line number="737" hits="2" branch="false"/>
            <line number="738" hits="2" branch="false"/>
            <line number="739" hits="2" branch="false"/>
            <line number="740" hits="2" branch="false"/>
            <line number="741" hits="1" branch="false"/>
            <line number="742" hits="1" branch="false"/>
            <line number="743" hits="1" branch="false"/>
            <line number="744" hits="1" branch="false"/>
            <line number="746" hits="2" branch="false"/>
            <line number="747" hits="1" branch="false"/>
            <line number="748" hits="1" branch="false"/>
            <line number="749" hits="1" branch="false"/>
            <line number="750" hits="1" branch="false"/>
            <line number="752" hits="2" branch="false"/>
            <line number="753" hits="1" branch="false"/>
            <line number="754" hits="1" branch="false"/>
            <line number="755" hits="1" branch="false"/>
            <line number="757" hits="1" branch="false"/>
            <line number="758" hits="1" branch="false"/>
            <line number="759" hits="1" branch="false"/>
            <line number="760" hits="1" branch="false"/>
            <line number="761" hits="1" branch="false"/>
            <line number="762" hits="1" branch="false"/>
            <line number="763" hits="1" branch="false"/>
            <line number="764" hits="1" branch="false"/>
            <line number="772" hits="2" branch="false"/>
            <line number="773" hits="2" branch="false"/>
            <line number="774" hits="2" branch="false"/>
            <line number="775" hits="2" branch="false"/>
            <line number="776" hits="2" branch="false"/>
            <line number="777" hits="2" branch="false"/>
            <line number="778" hits="2" branch="false"/>
            <line number="779" hits="2" branch="false"/>
            <line number="780" hits="2" branch="false"/>
            <line number="781" hits="2" branch="false"/>
            <line number="782" hits="2" branch="false"/>
            <line number="783" hits="2" branch="false"/>
            <line number="784" hits="2" branch="false"/>
            <line number="785" hits="2" branch="false"/>
            <line number="786" hits="2" branch="false"/>
            <line number="787" hits="2" branch="false"/>
            <line number="788" hits="2" branch="false"/>
            <line number="789" hits="2" branch="false"/>
            <line number="790" hits="2" branch="false"/>
            <line number="791" hits="2" branch="false"/>
            <line number="792" hits="2" branch="false"/>
            <line number="793" hits="2" branch="false"/>
            <line number="794" hits="2" branch="false"/>
            <line number="795" hits="2" branch="false"/>
            <line number="854" hits="14" branch="false"/>
            <line number="891" hits="3" branch="false"/>
            <line number="892" hits="3" branch="false"/>
            <line number="893" hits="3" branch="false"/>
            <line number="894" hits="2" branch="false"/>
            <line number="895" hits="3" branch="false"/>
            <line number="896" hits="1" branch="false"/>
            <line number="897" hits="3" branch="false"/>
            <line number="898" hits="3" branch="false"/>
            <line number="899" hits="2" branch="false"/>
            <line number="900" hits="2" branch="false"/>
            <line number="901" hits="1" branch="false"/>
            <line number="902" hits="1" branch="false"/>
            <line number="903" hits="1" branch="false"/>
            <line number="904" hits="1" branch="false"/>
            <line number="906" hits="2" branch="false"/>
            <line number="907" hits="2" branch="false"/>
            <line number="937" hits="5" branch="false"/>
            <line number="938" hits="5" branch="false"/>
          </lines>
        </class>
        <class name="HermesData-validate.R" filename="R/HermesData-validate.R" line-rate="1" branch-rate="0" complexity="0">
          <methods>
            <method name="validate_counts" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="30" hits="99" branch="false"/>
                <line number="31" hits="99" branch="false"/>
                <line number="32" hits="3" branch="false"/>
                <line number="34" hits="96" branch="false"/>
                <line number="35" hits="1" branch="false"/>
                <line number="38" hits="95" branch="false"/>
                <line number="40" hits="95" branch="false"/>
                <line number="41" hits="95" branch="false"/>
                <line number="42" hits="1" branch="false"/>
                <line number="44" hits="95" branch="false"/>
                <line number="45" hits="1" branch="false"/>
                <line number="47" hits="95" branch="false"/>
                <line number="48" hits="1" branch="false"/>
                <line number="51" hits="95" branch="false"/>
              </lines>
            </method>
            <method name="validate_cols" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="60" hits="207" branch="false"/>
                <line number="61" hits="12" branch="false"/>
                <line number="62" hits="12" branch="false"/>
                <line number="64" hits="195" branch="false"/>
              </lines>
            </method>
            <method name="validate_row_data" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="71" hits="99" branch="false"/>
                <line number="72" hits="99" branch="false"/>
                <line number="73" hits="99" branch="false"/>
              </lines>
            </method>
            <method name="validate_col_data" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="79" hits="99" branch="false"/>
                <line number="80" hits="99" branch="false"/>
                <line number="81" hits="99" branch="false"/>
              </lines>
            </method>
            <method name="validate_names" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="86" hits="101" branch="false"/>
                <line number="88" hits="101" branch="false"/>
                <line number="89" hits="4" branch="false"/>
                <line number="91" hits="101" branch="false"/>
                <line number="92" hits="4" branch="false"/>
                <line number="94" hits="101" branch="false"/>
                <line number="95" hits="2" branch="false"/>
                <line number="97" hits="101" branch="false"/>
                <line number="98" hits="2" branch="false"/>
                <line number="101" hits="101" branch="false"/>
              </lines>
            </method>
            <method name="validate_prefix" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="107" hits="98" branch="false"/>
                <line number="108" hits="98" branch="false"/>
                <line number="110" hits="98" branch="false"/>
                <line number="111" hits="3" branch="false"/>
                <line number="113" hits="95" branch="false"/>
                <line number="114" hits="1" branch="false"/>
                <line number="116" hits="95" branch="false"/>
                <line number="117" hits="95" branch="false"/>
                <line number="118" hits="1" branch="false"/>
                <line number="121" hits="98" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="30" hits="99" branch="false"/>
            <line number="31" hits="99" branch="false"/>
            <line number="32" hits="3" branch="false"/>
            <line number="34" hits="96" branch="false"/>
            <line number="35" hits="1" branch="false"/>
            <line number="38" hits="95" branch="false"/>
            <line number="40" hits="95" branch="false"/>
            <line number="41" hits="95" branch="false"/>
            <line number="42" hits="1" branch="false"/>
            <line number="44" hits="95" branch="false"/>
            <line number="45" hits="1" branch="false"/>
            <line number="47" hits="95" branch="false"/>
            <line number="48" hits="1" branch="false"/>
            <line number="51" hits="95" branch="false"/>
            <line number="60" hits="207" branch="false"/>
            <line number="61" hits="12" branch="false"/>
            <line number="62" hits="12" branch="false"/>
            <line number="64" hits="195" branch="false"/>
            <line number="71" hits="99" branch="false"/>
            <line number="72" hits="99" branch="false"/>
            <line number="73" hits="99" branch="false"/>
            <line number="79" hits="99" branch="false"/>
            <line number="80" hits="99" branch="false"/>
            <line number="81" hits="99" branch="false"/>
            <line number="86" hits="101" branch="false"/>
            <line number="88" hits="101" branch="false"/>
            <line number="89" hits="4" branch="false"/>
            <line number="91" hits="101" branch="false"/>
            <line number="92" hits="4" branch="false"/>
            <line number="94" hits="101" branch="false"/>
            <line number="95" hits="2" branch="false"/>
            <line number="97" hits="101" branch="false"/>
            <line number="98" hits="2" branch="false"/>
            <line number="101" hits="101" branch="false"/>
            <line number="107" hits="98" branch="false"/>
            <line number="108" hits="98" branch="false"/>
            <line number="110" hits="98" branch="false"/>
            <line number="111" hits="3" branch="false"/>
            <line number="113" hits="95" branch="false"/>
            <line number="114" hits="1" branch="false"/>
            <line number="116" hits="95" branch="false"/>
            <line number="117" hits="95" branch="false"/>
            <line number="118" hits="1" branch="false"/>
            <line number="121" hits="98" branch="false"/>
          </lines>
        </class>
        <class name="join_cdisc.R" filename="R/join_cdisc.R" line-rate="1" branch-rate="0" complexity="0">
          <methods>
            <method name="col_data_with_genes" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="26" hits="2" branch="false"/>
                <line number="27" hits="2" branch="false"/>
                <line number="28" hits="2" branch="false"/>
                <line number="30" hits="2" branch="false"/>
                <line number="31" hits="2" branch="false"/>
                <line number="32" hits="2" branch="false"/>
                <line number="34" hits="2" branch="false"/>
                <line number="35" hits="2" branch="false"/>
                <line number="36" hits="2" branch="false"/>
                <line number="37" hits="2" branch="false"/>
                <line number="38" hits="2" branch="false"/>
                <line number="39" hits="2" branch="false"/>
                <line number="40" hits="2" branch="false"/>
                <line number="41" hits="2" branch="false"/>
                <line number="42" hits="2" branch="false"/>
                <line number="43" hits="2" branch="false"/>
                <line number="44" hits="2" branch="false"/>
              </lines>
            </method>
            <method name="inner_join_cdisc" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="76" hits="5" branch="false"/>
                <line number="77" hits="5" branch="false"/>
                <line number="78" hits="5" branch="false"/>
                <line number="79" hits="5" branch="false"/>
                <line number="81" hits="5" branch="false"/>
                <line number="82" hits="5" branch="false"/>
                <line number="83" hits="5" branch="false"/>
                <line number="86" hits="5" branch="false"/>
                <line number="87" hits="5" branch="false"/>
                <line number="88" hits="5" branch="false"/>
                <line number="89" hits="5" branch="false"/>
                <line number="92" hits="5" branch="false"/>
                <line number="93" hits="5" branch="false"/>
                <line number="94" hits="5" branch="false"/>
                <line number="95" hits="5" branch="false"/>
                <line number="96" hits="1" branch="false"/>
                <line number="97" hits="1" branch="false"/>
                <line number="98" hits="1" branch="false"/>
                <line number="99" hits="1" branch="false"/>
                <line number="102" hits="5" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="26" hits="2" branch="false"/>
            <line number="27" hits="2" branch="false"/>
            <line number="28" hits="2" branch="false"/>
            <line number="30" hits="2" branch="false"/>
            <line number="31" hits="2" branch="false"/>
            <line number="32" hits="2" branch="false"/>
            <line number="34" hits="2" branch="false"/>
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            <line number="36" hits="2" branch="false"/>
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            <line number="96" hits="1" branch="false"/>
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            <line number="98" hits="1" branch="false"/>
            <line number="99" hits="1" branch="false"/>
            <line number="102" hits="5" branch="false"/>
          </lines>
        </class>
        <class name="normalization.R" filename="R/normalization.R" line-rate="0.98" branch-rate="0" complexity="0">
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              <lines>
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                <line number="29" hits="62" branch="false"/>
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                <line number="38" hits="57" branch="false"/>
                <line number="39" hits="57" branch="false"/>
              </lines>
            </method>
            <method name="AnyHermesData" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="125" hits="58" branch="false"/>
                <line number="127" hits="13" branch="false"/>
                <line number="128" hits="13" branch="false"/>
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            </method>
            <method name="h_cpm" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="149" hits="15" branch="false"/>
                <line number="150" hits="15" branch="false"/>
                <line number="151" hits="15" branch="false"/>
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            <method name="h_rpkm" signature="" line-rate="1" branch-rate="0" complexity="0">
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                <line number="175" hits="29" branch="false"/>
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            </method>
            <method name="h_tpm" signature="" line-rate="0.833333333333333" branch-rate="0" complexity="0">
              <lines>
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                <line number="189" hits="15" branch="false"/>
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                <line number="192" hits="14" branch="false"/>
                <line number="194" hits="0" branch="false"/>
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            <method name="h_voom" signature="" line-rate="0.928571428571429" branch-rate="0" complexity="0">
              <lines>
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                <line number="213" hits="16" branch="false"/>
                <line number="214" hits="2" branch="false"/>
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                <line number="220" hits="14" branch="false"/>
                <line number="221" hits="14" branch="false"/>
                <line number="223" hits="0" branch="false"/>
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            <method name="h_vst" signature="" line-rate="1" branch-rate="0" complexity="0">
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                <line number="252" hits="4" branch="false"/>
                <line number="253" hits="15" branch="false"/>
                <line number="254" hits="15" branch="false"/>
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            </method>
            <method name="h_rlog" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="267" hits="8" branch="false"/>
                <line number="268" hits="8" branch="false"/>
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                <line number="272" hits="4" branch="false"/>
                <line number="273" hits="4" branch="false"/>
                <line number="274" hits="4" branch="false"/>
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            </method>
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        </class>
        <class name="pca_cor_samplevar.R" filename="R/pca_cor_samplevar.R" line-rate="1" branch-rate="0" complexity="0">
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            <method name="h_pca_var_rsquared" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="38" hits="165" branch="false"/>
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                <line number="41" hits="165" branch="false"/>
                <line number="42" hits="165" branch="false"/>
                <line number="43" hits="162" branch="false"/>
                <line number="44" hits="162" branch="false"/>
                <line number="45" hits="162" branch="false"/>
                <line number="46" hits="1" branch="false"/>
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                <line number="52" hits="162" branch="false"/>
                <line number="53" hits="162" branch="false"/>
                <line number="54" hits="162" branch="false"/>
                <line number="55" hits="162" branch="false"/>
                <line number="56" hits="162" branch="false"/>
                <line number="57" hits="162" branch="false"/>
                <line number="58" hits="162" branch="false"/>
              </lines>
            </method>
            <method name="h_pca_df_r2_matrix" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="108" hits="5" branch="false"/>
                <line number="109" hits="5" branch="false"/>
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                <line number="116" hits="4" branch="false"/>
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                <line number="118" hits="4" branch="false"/>
                <line number="120" hits="4" branch="false"/>
                <line number="121" hits="4" branch="false"/>
                <line number="123" hits="4" branch="false"/>
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                <line number="135" hits="4" branch="false"/>
                <line number="136" hits="4" branch="false"/>
                <line number="137" hits="4" branch="false"/>
              </lines>
            </method>
            <method name="HermesDataPca" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="177" hits="4" branch="false"/>
                <line number="178" hits="4" branch="false"/>
                <line number="179" hits="4" branch="false"/>
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                <line number="181" hits="4" branch="false"/>
                <line number="182" hits="4" branch="false"/>
                <line number="183" hits="3" branch="false"/>
                <line number="184" hits="3" branch="false"/>
                <line number="185" hits="3" branch="false"/>
              </lines>
            </method>
            <method name="HermesDataPcaCor" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="235" hits="1" branch="false"/>
                <line number="236" hits="1" branch="false"/>
                <line number="237" hits="1" branch="false"/>
                <line number="238" hits="1" branch="false"/>
                <line number="239" hits="1" branch="false"/>
                <line number="240" hits="1" branch="false"/>
                <line number="241" hits="1" branch="false"/>
              </lines>
            </method>
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            <line number="185" hits="3" branch="false"/>
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            <line number="236" hits="1" branch="false"/>
            <line number="237" hits="1" branch="false"/>
            <line number="238" hits="1" branch="false"/>
            <line number="239" hits="1" branch="false"/>
            <line number="240" hits="1" branch="false"/>
            <line number="241" hits="1" branch="false"/>
          </lines>
        </class>
        <class name="pca.R" filename="R/pca.R" line-rate="1" branch-rate="0" complexity="0">
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            <method name="calc_pca" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
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                <line number="52" hits="14" branch="false"/>
                <line number="53" hits="14" branch="false"/>
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                <line number="55" hits="14" branch="false"/>
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                <line number="58" hits="10" branch="false"/>
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                <line number="60" hits="2" branch="false"/>
                <line number="61" hits="2" branch="false"/>
                <line number="62" hits="2" branch="false"/>
                <line number="63" hits="2" branch="false"/>
                <line number="64" hits="2" branch="false"/>
                <line number="65" hits="2" branch="false"/>
                <line number="66" hits="2" branch="false"/>
                <line number="67" hits="2" branch="false"/>
                <line number="68" hits="12" branch="false"/>
                <line number="70" hits="12" branch="false"/>
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                <line number="78" hits="11" branch="false"/>
                <line number="79" hits="11" branch="false"/>
                <line number="80" hits="11" branch="false"/>
                <line number="82" hits="11" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="51" hits="14" branch="false"/>
            <line number="52" hits="14" branch="false"/>
            <line number="53" hits="14" branch="false"/>
            <line number="54" hits="14" branch="false"/>
            <line number="55" hits="14" branch="false"/>
            <line number="57" hits="12" branch="false"/>
            <line number="58" hits="10" branch="false"/>
            <line number="59" hits="12" branch="false"/>
            <line number="60" hits="2" branch="false"/>
            <line number="61" hits="2" branch="false"/>
            <line number="62" hits="2" branch="false"/>
            <line number="63" hits="2" branch="false"/>
            <line number="64" hits="2" branch="false"/>
            <line number="65" hits="2" branch="false"/>
            <line number="66" hits="2" branch="false"/>
            <line number="67" hits="2" branch="false"/>
            <line number="68" hits="12" branch="false"/>
            <line number="70" hits="12" branch="false"/>
            <line number="71" hits="11" branch="false"/>
            <line number="72" hits="11" branch="false"/>
            <line number="73" hits="11" branch="false"/>
            <line number="75" hits="11" branch="false"/>
            <line number="76" hits="11" branch="false"/>
            <line number="77" hits="11" branch="false"/>
            <line number="78" hits="11" branch="false"/>
            <line number="79" hits="11" branch="false"/>
            <line number="80" hits="11" branch="false"/>
            <line number="82" hits="11" branch="false"/>
          </lines>
        </class>
        <class name="quality.R" filename="R/quality.R" line-rate="0.96" branch-rate="0" complexity="0">
          <methods>
            <method name="control_quality" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="36" hits="33" branch="false"/>
                <line number="37" hits="33" branch="false"/>
                <line number="38" hits="33" branch="false"/>
                <line number="39" hits="29" branch="false"/>
                <line number="40" hits="24" branch="false"/>
                <line number="41" hits="19" branch="false"/>
                <line number="43" hits="15" branch="false"/>
                <line number="44" hits="15" branch="false"/>
                <line number="45" hits="15" branch="false"/>
                <line number="46" hits="15" branch="false"/>
                <line number="47" hits="15" branch="false"/>
                <line number="48" hits="15" branch="false"/>
              </lines>
            </method>
            <method name="add_quality_flags" signature="" line-rate="0.785714285714286" branch-rate="0" complexity="0">
              <lines>
                <line number="103" hits="6" branch="false"/>
                <line number="104" hits="6" branch="false"/>
                <line number="105" hits="6" branch="false"/>
                <line number="106" hits="6" branch="false"/>
                <line number="107" hits="3" branch="false"/>
                <line number="108" hits="3" branch="false"/>
                <line number="109" hits="0" branch="false"/>
                <line number="110" hits="0" branch="false"/>
                <line number="112" hits="0" branch="false"/>
                <line number="116" hits="3" branch="false"/>
                <line number="117" hits="2" branch="false"/>
                <line number="118" hits="2" branch="false"/>
                <line number="120" hits="2" branch="false"/>
                <line number="122" hits="2" branch="false"/>
              </lines>
            </method>
            <method name="h_low_expression_flag" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="141" hits="10" branch="false"/>
                <line number="142" hits="10" branch="false"/>
                <line number="143" hits="10" branch="false"/>
                <line number="144" hits="10" branch="false"/>
                <line number="145" hits="5" branch="false"/>
                <line number="146" hits="5" branch="false"/>
                <line number="147" hits="5" branch="false"/>
                <line number="148" hits="5" branch="false"/>
              </lines>
            </method>
            <method name="h_low_depth_flag" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="164" hits="9" branch="false"/>
                <line number="165" hits="9" branch="false"/>
                <line number="166" hits="9" branch="false"/>
                <line number="167" hits="9" branch="false"/>
                <line number="168" hits="5" branch="false"/>
                <line number="169" hits="5" branch="false"/>
                <line number="170" hits="3" branch="false"/>
                <line number="171" hits="3" branch="false"/>
                <line number="173" hits="5" branch="false"/>
              </lines>
            </method>
            <method name="h_tech_failure_flag" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="189" hits="9" branch="false"/>
                <line number="190" hits="9" branch="false"/>
                <line number="191" hits="9" branch="false"/>
                <line number="192" hits="9" branch="false"/>
                <line number="193" hits="5" branch="false"/>
                <line number="195" hits="5" branch="false"/>
                <line number="196" hits="4" branch="false"/>
                <line number="197" hits="4" branch="false"/>
                <line number="199" hits="1" branch="false"/>
                <line number="200" hits="1" branch="false"/>
                <line number="201" hits="1" branch="false"/>
                <line number="202" hits="1" branch="false"/>
              </lines>
            </method>
            <method name="get_tech_failure" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="211" hits="24" branch="false"/>
                <line number="212" hits="22" branch="false"/>
                <line number="213" hits="22" branch="false"/>
                <line number="214" hits="22" branch="false"/>
              </lines>
            </method>
            <method name="get_low_depth" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="222" hits="22" branch="false"/>
                <line number="223" hits="20" branch="false"/>
                <line number="224" hits="20" branch="false"/>
                <line number="225" hits="20" branch="false"/>
              </lines>
            </method>
            <method name="get_low_expression" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="233" hits="22" branch="false"/>
                <line number="234" hits="20" branch="false"/>
                <line number="235" hits="20" branch="false"/>
                <line number="236" hits="20" branch="false"/>
              </lines>
            </method>
            <method name="set_tech_failure" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="262" hits="5" branch="false"/>
                <line number="263" hits="3" branch="false"/>
                <line number="264" hits="3" branch="false"/>
                <line number="265" hits="3" branch="false"/>
                <line number="266" hits="3" branch="false"/>
                <line number="267" hits="1" branch="false"/>
                <line number="268" hits="1" branch="false"/>
                <line number="269" hits="1" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="36" hits="33" branch="false"/>
            <line number="37" hits="33" branch="false"/>
            <line number="38" hits="33" branch="false"/>
            <line number="39" hits="29" branch="false"/>
            <line number="40" hits="24" branch="false"/>
            <line number="41" hits="19" branch="false"/>
            <line number="43" hits="15" branch="false"/>
            <line number="44" hits="15" branch="false"/>
            <line number="45" hits="15" branch="false"/>
            <line number="46" hits="15" branch="false"/>
            <line number="47" hits="15" branch="false"/>
            <line number="48" hits="15" branch="false"/>
            <line number="103" hits="6" branch="false"/>
            <line number="104" hits="6" branch="false"/>
            <line number="105" hits="6" branch="false"/>
            <line number="106" hits="6" branch="false"/>
            <line number="107" hits="3" branch="false"/>
            <line number="108" hits="3" branch="false"/>
            <line number="109" hits="0" branch="false"/>
            <line number="110" hits="0" branch="false"/>
            <line number="112" hits="0" branch="false"/>
            <line number="116" hits="3" branch="false"/>
            <line number="117" hits="2" branch="false"/>
            <line number="118" hits="2" branch="false"/>
            <line number="120" hits="2" branch="false"/>
            <line number="122" hits="2" branch="false"/>
            <line number="141" hits="10" branch="false"/>
            <line number="142" hits="10" branch="false"/>
            <line number="143" hits="10" branch="false"/>
            <line number="144" hits="10" branch="false"/>
            <line number="145" hits="5" branch="false"/>
            <line number="146" hits="5" branch="false"/>
            <line number="147" hits="5" branch="false"/>
            <line number="148" hits="5" branch="false"/>
            <line number="164" hits="9" branch="false"/>
            <line number="165" hits="9" branch="false"/>
            <line number="166" hits="9" branch="false"/>
            <line number="167" hits="9" branch="false"/>
            <line number="168" hits="5" branch="false"/>
            <line number="169" hits="5" branch="false"/>
            <line number="170" hits="3" branch="false"/>
            <line number="171" hits="3" branch="false"/>
            <line number="173" hits="5" branch="false"/>
            <line number="189" hits="9" branch="false"/>
            <line number="190" hits="9" branch="false"/>
            <line number="191" hits="9" branch="false"/>
            <line number="192" hits="9" branch="false"/>
            <line number="193" hits="5" branch="false"/>
            <line number="195" hits="5" branch="false"/>
            <line number="196" hits="4" branch="false"/>
            <line number="197" hits="4" branch="false"/>
            <line number="199" hits="1" branch="false"/>
            <line number="200" hits="1" branch="false"/>
            <line number="201" hits="1" branch="false"/>
            <line number="202" hits="1" branch="false"/>
            <line number="211" hits="24" branch="false"/>
            <line number="212" hits="22" branch="false"/>
            <line number="213" hits="22" branch="false"/>
            <line number="214" hits="22" branch="false"/>
            <line number="222" hits="22" branch="false"/>
            <line number="223" hits="20" branch="false"/>
            <line number="224" hits="20" branch="false"/>
            <line number="225" hits="20" branch="false"/>
            <line number="233" hits="22" branch="false"/>
            <line number="234" hits="20" branch="false"/>
            <line number="235" hits="20" branch="false"/>
            <line number="236" hits="20" branch="false"/>
            <line number="262" hits="5" branch="false"/>
            <line number="263" hits="3" branch="false"/>
            <line number="264" hits="3" branch="false"/>
            <line number="265" hits="3" branch="false"/>
            <line number="266" hits="3" branch="false"/>
            <line number="267" hits="1" branch="false"/>
            <line number="268" hits="1" branch="false"/>
            <line number="269" hits="1" branch="false"/>
          </lines>
        </class>
        <class name="top_genes.R" filename="R/top_genes.R" line-rate="1" branch-rate="0" complexity="0">
          <methods>
            <method name="top_genes" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="46" hits="21" branch="false"/>
                <line number="47" hits="21" branch="false"/>
                <line number="48" hits="21" branch="false"/>
                <line number="49" hits="21" branch="false"/>
                <line number="50" hits="21" branch="false"/>
                <line number="51" hits="21" branch="false"/>
                <line number="53" hits="16" branch="false"/>
                <line number="54" hits="16" branch="false"/>
                <line number="55" hits="16" branch="false"/>
                <line number="56" hits="16" branch="false"/>
                <line number="57" hits="16" branch="false"/>
                <line number="58" hits="16" branch="false"/>
                <line number="59" hits="16" branch="false"/>
                <line number="61" hits="14" branch="false"/>
                <line number="62" hits="14" branch="false"/>
                <line number="63" hits="14" branch="false"/>
                <line number="64" hits="14" branch="false"/>
                <line number="65" hits="14" branch="false"/>
                <line number="66" hits="14" branch="false"/>
                <line number="67" hits="14" branch="false"/>
                <line number="68" hits="14" branch="false"/>
                <line number="70" hits="14" branch="false"/>
                <line number="71" hits="4" branch="false"/>
                <line number="72" hits="4" branch="false"/>
                <line number="73" hits="4" branch="false"/>
                <line number="74" hits="4" branch="false"/>
                <line number="75" hits="4" branch="false"/>
                <line number="76" hits="1" branch="false"/>
                <line number="77" hits="14" branch="false"/>
                <line number="78" hits="10" branch="false"/>
                <line number="79" hits="9" branch="false"/>
                <line number="80" hits="14" branch="false"/>
                <line number="81" hits="10" branch="false"/>
                <line number="83" hits="10" branch="false"/>
                <line number="84" hits="10" branch="false"/>
                <line number="85" hits="10" branch="false"/>
                <line number="86" hits="10" branch="false"/>
                <line number="87" hits="10" branch="false"/>
              </lines>
            </method>
            <method name="HermesDataTopGenes" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="125" hits="2" branch="false"/>
                <line number="126" hits="2" branch="false"/>
                <line number="127" hits="2" branch="false"/>
                <line number="128" hits="2" branch="false"/>
                <line number="129" hits="2" branch="false"/>
                <line number="131" hits="2" branch="false"/>
                <line number="133" hits="2" branch="false"/>
                <line number="134" hits="2" branch="false"/>
                <line number="135" hits="2" branch="false"/>
                <line number="136" hits="2" branch="false"/>
                <line number="137" hits="2" branch="false"/>
                <line number="138" hits="2" branch="false"/>
                <line number="139" hits="2" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="46" hits="21" branch="false"/>
            <line number="47" hits="21" branch="false"/>
            <line number="48" hits="21" branch="false"/>
            <line number="49" hits="21" branch="false"/>
            <line number="50" hits="21" branch="false"/>
            <line number="51" hits="21" branch="false"/>
            <line number="53" hits="16" branch="false"/>
            <line number="54" hits="16" branch="false"/>
            <line number="55" hits="16" branch="false"/>
            <line number="56" hits="16" branch="false"/>
            <line number="57" hits="16" branch="false"/>
            <line number="58" hits="16" branch="false"/>
            <line number="59" hits="16" branch="false"/>
            <line number="61" hits="14" branch="false"/>
            <line number="62" hits="14" branch="false"/>
            <line number="63" hits="14" branch="false"/>
            <line number="64" hits="14" branch="false"/>
            <line number="65" hits="14" branch="false"/>
            <line number="66" hits="14" branch="false"/>
            <line number="67" hits="14" branch="false"/>
            <line number="68" hits="14" branch="false"/>
            <line number="70" hits="14" branch="false"/>
            <line number="71" hits="4" branch="false"/>
            <line number="72" hits="4" branch="false"/>
            <line number="73" hits="4" branch="false"/>
            <line number="74" hits="4" branch="false"/>
            <line number="75" hits="4" branch="false"/>
            <line number="76" hits="1" branch="false"/>
            <line number="77" hits="14" branch="false"/>
            <line number="78" hits="10" branch="false"/>
            <line number="79" hits="9" branch="false"/>
            <line number="80" hits="14" branch="false"/>
            <line number="81" hits="10" branch="false"/>
            <line number="83" hits="10" branch="false"/>
            <line number="84" hits="10" branch="false"/>
            <line number="85" hits="10" branch="false"/>
            <line number="86" hits="10" branch="false"/>
            <line number="87" hits="10" branch="false"/>
            <line number="125" hits="2" branch="false"/>
            <line number="126" hits="2" branch="false"/>
            <line number="127" hits="2" branch="false"/>
            <line number="128" hits="2" branch="false"/>
            <line number="129" hits="2" branch="false"/>
            <line number="131" hits="2" branch="false"/>
            <line number="133" hits="2" branch="false"/>
            <line number="134" hits="2" branch="false"/>
            <line number="135" hits="2" branch="false"/>
            <line number="136" hits="2" branch="false"/>
            <line number="137" hits="2" branch="false"/>
            <line number="138" hits="2" branch="false"/>
            <line number="139" hits="2" branch="false"/>
          </lines>
        </class>
        <class name="utils.R" filename="R/utils.R" line-rate="1" branch-rate="0" complexity="0">
          <methods>
            <method name="h_df_factors_with_explicit_na" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="51" hits="16" branch="false"/>
                <line number="52" hits="15" branch="false"/>
                <line number="55" hits="15" branch="false"/>
                <line number="56" hits="15" branch="false"/>
                <line number="57" hits="15" branch="false"/>
                <line number="58" hits="15" branch="false"/>
                <line number="59" hits="15" branch="false"/>
                <line number="60" hits="15" branch="false"/>
                <line number="63" hits="15" branch="false"/>
                <line number="64" hits="15" branch="false"/>
                <line number="65" hits="15" branch="false"/>
                <line number="66" hits="15" branch="false"/>
                <line number="67" hits="15" branch="false"/>
                <line number="68" hits="15" branch="false"/>
                <line number="71" hits="15" branch="false"/>
                <line number="72" hits="15" branch="false"/>
                <line number="73" hits="15" branch="false"/>
                <line number="74" hits="15" branch="false"/>
                <line number="75" hits="15" branch="false"/>
                <line number="76" hits="15" branch="false"/>
                <line number="78" hits="15" branch="false"/>
              </lines>
            </method>
            <method name="df_cols_to_factor" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="111" hits="8" branch="false"/>
                <line number="112" hits="8" branch="false"/>
                <line number="113" hits="8" branch="false"/>
                <line number="114" hits="8" branch="false"/>
                <line number="115" hits="8" branch="false"/>
                <line number="116" hits="8" branch="false"/>
                <line number="117" hits="8" branch="false"/>
                <line number="118" hits="8" branch="false"/>
                <line number="119" hits="8" branch="false"/>
                <line number="120" hits="8" branch="false"/>
                <line number="121" hits="8" branch="false"/>
                <line number="122" hits="8" branch="false"/>
                <line number="123" hits="8" branch="false"/>
                <line number="124" hits="8" branch="false"/>
                <line number="125" hits="8" branch="false"/>
                <line number="126" hits="8" branch="false"/>
                <line number="128" hits="8" branch="false"/>
              </lines>
            </method>
            <method name="all_na" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="138" hits="308" branch="false"/>
              </lines>
            </method>
            <method name="h_short_list" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="162" hits="15" branch="false"/>
                <line number="163" hits="15" branch="false"/>
                <line number="164" hits="14" branch="false"/>
                <line number="166" hits="13" branch="false"/>
                <line number="167" hits="13" branch="false"/>
                <line number="168" hits="3" branch="false"/>
                <line number="170" hits="13" branch="false"/>
              </lines>
            </method>
            <method name="h_parens" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="192" hits="21" branch="false"/>
                <line number="193" hits="18" branch="false"/>
              </lines>
            </method>
            <method name="colPrinComp1" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="223" hits="2" branch="false"/>
                <line number="224" hits="1" branch="false"/>
                <line number="225" hits="1" branch="false"/>
                <line number="227" hits="1" branch="false"/>
                <line number="228" hits="1" branch="false"/>
                <line number="230" hits="1" branch="false"/>
                <line number="231" hits="1" branch="false"/>
              </lines>
            </method>
            <method name="colMeanZscores" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="255" hits="1" branch="false"/>
                <line number="257" hits="1" branch="false"/>
                <line number="258" hits="1" branch="false"/>
                <line number="259" hits="1" branch="false"/>
                <line number="260" hits="1" branch="false"/>
                <line number="261" hits="1" branch="false"/>
                <line number="262" hits="1" branch="false"/>
                <line number="263" hits="1" branch="false"/>
                <line number="264" hits="1" branch="false"/>
                <line number="265" hits="1" branch="false"/>
                <line number="266" hits="1" branch="false"/>
                <line number="267" hits="1" branch="false"/>
              </lines>
            </method>
            <method name="wrap_in_mae" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="290" hits="3" branch="false"/>
                <line number="291" hits="3" branch="false"/>
                <line number="292" hits="3" branch="false"/>
                <line number="293" hits="3" branch="false"/>
              </lines>
            </method>
            <method name="h_all_duplicated" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="310" hits="29" branch="false"/>
                <line number="311" hits="29" branch="false"/>
                <line number="312" hits="29" branch="false"/>
              </lines>
            </method>
            <method name="cut_quantile" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="341" hits="9" branch="false"/>
                <line number="342" hits="9" branch="false"/>
                <line number="343" hits="9" branch="false"/>
                <line number="345" hits="9" branch="false"/>
                <line number="346" hits="9" branch="false"/>
                <line number="347" hits="9" branch="false"/>
                <line number="348" hits="9" branch="false"/>
                <line number="350" hits="9" branch="false"/>
                <line number="351" hits="1" branch="false"/>
                <line number="354" hits="8" branch="false"/>
                <line number="355" hits="8" branch="false"/>
                <line number="356" hits="8" branch="false"/>
                <line number="357" hits="8" branch="false"/>
                <line number="358" hits="8" branch="false"/>
                <line number="359" hits="8" branch="false"/>
                <line number="360" hits="8" branch="false"/>
                <line number="361" hits="1" branch="false"/>
                <line number="364" hits="7" branch="false"/>
                <line number="365" hits="7" branch="false"/>
                <line number="366" hits="7" branch="false"/>
                <line number="367" hits="7" branch="false"/>
                <line number="370" hits="7" branch="false"/>
              </lines>
            </method>
            <method name="cat_with_newline" signature="" line-rate="1" branch-rate="0" complexity="0">
              <lines>
                <line number="391" hits="10" branch="false"/>
                <line number="392" hits="10" branch="false"/>
              </lines>
            </method>
          </methods>
          <lines>
            <line number="51" hits="16" branch="false"/>
            <line number="52" hits="15" branch="false"/>
            <line number="55" hits="15" branch="false"/>
            <line number="56" hits="15" branch="false"/>
            <line number="57" hits="15" branch="false"/>
            <line number="58" hits="15" branch="false"/>
            <line number="59" hits="15" branch="false"/>
            <line number="60" hits="15" branch="false"/>
            <line number="63" hits="15" branch="false"/>
            <line number="64" hits="15" branch="false"/>
            <line number="65" hits="15" branch="false"/>
            <line number="66" hits="15" branch="false"/>
            <line number="67" hits="15" branch="false"/>
            <line number="68" hits="15" branch="false"/>
            <line number="71" hits="15" branch="false"/>
            <line number="72" hits="15" branch="false"/>
            <line number="73" hits="15" branch="false"/>
            <line number="74" hits="15" branch="false"/>
            <line number="75" hits="15" branch="false"/>
            <line number="76" hits="15" branch="false"/>
            <line number="78" hits="15" branch="false"/>
            <line number="111" hits="8" branch="false"/>
            <line number="112" hits="8" branch="false"/>
            <line number="113" hits="8" branch="false"/>
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