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‎docs/PascalX.html‎

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‎docs/_sources/index.rst.txt‎

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* For all technical issues (bug reports, etc.), please open a ticket on the `GitHub <https://github.com/BergmannLab/PascalX/issues>`_ page.
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* For general inquiries, please contact the main contributor: Daniel.Krefl(@unil.ch)

‎docs/genindex.html‎

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<h1 id="index">Index</h1>
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<div class="genindex-jumpbox">
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<a href="#C"><strong>C</strong></a>
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<a href="#A"><strong>A</strong></a>
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| <a href="#C"><strong>C</strong></a>
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| <a href="#D"><strong>D</strong></a>
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| <a href="#G"><strong>G</strong></a>
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| <a href="#I"><strong>I</strong></a>
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| <a href="#J"><strong>J</strong></a>
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| <a href="#L"><strong>L</strong></a>
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| <a href="#M"><strong>M</strong></a>
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| <a href="#O"><strong>O</strong></a>
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| <a href="#P"><strong>P</strong></a>
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| <a href="#R"><strong>R</strong></a>
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| <a href="#S"><strong>S</strong></a>
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| <a href="#T"><strong>T</strong></a>
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| <a href="#W"><strong>W</strong></a>
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| <a href="#Z"><strong>Z</strong></a>
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</div>
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<h2 id="A">A</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum.activateFails">activateFails() (PascalX.genescorer.chi2sum method)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="C">C</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.pathway.chi2perm">chi2perm (class in PascalX.pathway)</a>
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</li>
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<li><a href="PascalX.html#PascalX.pathway.chi2rank">chi2rank (class in PascalX.pathway)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genexpr.genexpr.chi2rank">chi2rank() (PascalX.genexpr.genexpr method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.pathway.chi2rank">chi2rank (class in PascalX.pathway)</a>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum">chi2sum (class in PascalX.genescorer)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.clean">clean() (PascalX.genescorer.genescorer method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.snpdb.db.close">close() (PascalX.snpdb.db method)</a>
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</li>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genome.genome.gene_info">gene_info() (PascalX.genome.genome method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer">genescorer (class in PascalX.genescorer)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genexpr.genexpr">genexpr (class in PascalX.genexpr)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genome.genome">genome (class in PascalX.genome)</a>
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</li>
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<li><a href="PascalX.html#PascalX.snpdb.db.get">get() (PascalX.snpdb.db method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genome.genome.get_ensembl_annotation">get_ensembl_annotation() (PascalX.genome.genome method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.get_geneinfo">get_geneinfo() (PascalX.genescorer.genescorer method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genexpr.genexpr.get_GTEX_expr">get_GTEX_expr() (PascalX.genexpr.genexpr method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.pathway.chi2perm.get_sigpathways">get_sigpathways() (PascalX.pathway.chi2perm method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.pathway.chi2rank.get_sigpathways">(PascalX.pathway.chi2rank method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.refpanel.refpanel.getChrSNPs">getChrSNPs() (PascalX.refpanel.refpanel method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.get_topscores">get_topscores() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.get_topscores">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.get_topscores">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.refpanel.refpanel.getChrSNPs">getChrSNPs() (PascalX.refpanel.refpanel method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.snpdb.db.getKeys">getKeys() (PascalX.snpdb.db method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.snpdb.db.getPosatSNPs">getPosatSNPs() (PascalX.snpdb.db method)</a>
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<h2 id="J">J</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.jointlyRank">jointlyRank() (PascalX.xscorer.rsum method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.jointlyRank">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.jointlyRank_mapper">jointlyRank_mapper() (PascalX.xscorer.rsum method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.jointlyRank_mapper">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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</ul></td>
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</tr></table>
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<h2 id="L">L</h2>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genome.genome.load_genome">load_genome() (PascalX.genome.genome method)</a>
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<li><a href="PascalX.html#PascalX.genexpr.genexpr.load_expr">load_expr() (PascalX.genexpr.genexpr method)</a>
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<li><a href="PascalX.html#PascalX.mapper.mapper.load_mapping">load_mapping() (PascalX.mapper.mapper method)</a>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.load_genome">load_genome() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.genexpr.genexpr.load_genome">(PascalX.genexpr.genexpr method)</a>
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<li><a href="PascalX.html#PascalX.pathway.chi2perm.load_modules">load_modules() (PascalX.pathway.chi2perm method)</a>
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<li><a href="PascalX.html#PascalX.genome.genome.load_genome">(PascalX.genome.genome method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.load_genome">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.load_genome">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.load_GWAS">load_GWAS() (PascalX.genescorer.genescorer method)</a>
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<li><a href="PascalX.html#PascalX.pathway.chi2rank.load_modules">(PascalX.pathway.chi2rank method)</a>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.load_GWAS">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.load_GWAS">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.load_mapping">load_mapping() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.mapper.mapper.load_mapping">(PascalX.mapper.mapper method)</a>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.load_mapping">(PascalX.xscorer.rsum method)</a>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.load_mapping">(PascalX.xscorer.zsum method)</a>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.pathway.chi2perm.load_modules">load_modules() (PascalX.pathway.chi2perm method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.pathway.chi2rank.load_modules">(PascalX.pathway.chi2rank method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.refpanel.refpanel.load_pos_reference">load_pos_reference() (PascalX.refpanel.refpanel method)</a>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.load_refpanel">load_refpanel() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.load_refpanel">(PascalX.xscorer.rsum method)</a>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.load_refpanel">(PascalX.xscorer.zsum method)</a>
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</ul></li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.load_scores">load_scores() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.load_scores">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.load_scores">(PascalX.xscorer.zsum method)</a>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.matchAlleles">matchAlleles() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.matchAlleles">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.matchAlleles">(PascalX.xscorer.zsum method)</a>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.matchAlleles_mapper">matchAlleles_mapper() (PascalX.xscorer.rsum method)</a>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.matchAlleles_mapper">(PascalX.xscorer.zsum method)</a>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum.plot_genesnps">plot_genesnps() (PascalX.genescorer.chi2sum method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.plot_genesnps">(PascalX.xscorer.rsum method)</a>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.plot_genesnps">(PascalX.xscorer.zsum method)</a>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.plot_Manhattan">plot_Manhattan() (PascalX.genescorer.genescorer method)</a>
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</li>
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</ul></td>
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</tr></table>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.rank">rank() (PascalX.genescorer.genescorer method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.rank_mapper">rank_mapper() (PascalX.genescorer.genescorer method)</a>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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</li>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum.rescore">rescore() (PascalX.genescorer.chi2sum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.rsum">rsum (class in PascalX.xscorer)</a>
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<h2 id="S">S</h2>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.save_GWAS">save_GWAS() (PascalX.genescorer.genescorer method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.save_scores">save_scores() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.save_scores">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.save_scores">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum.score">score() (PascalX.genescorer.chi2sum method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.genescorer.wchi2sum.score">(PascalX.genescorer.wchi2sum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.pathway.chi2perm.score">(PascalX.pathway.chi2perm method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.pathway.chi2rank.score">(PascalX.pathway.chi2rank method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.score">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.score">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.score_all">score_all() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.score_all">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.score_all">(PascalX.xscorer.zsum method)</a>
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</ul></li>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.genescorer.genescorer.score_chr">score_chr() (PascalX.genescorer.genescorer method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.score_chr">(PascalX.xscorer.rsum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.score_chr">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum.score_gene_bulk_chr">score_gene_bulk_chr() (PascalX.genescorer.chi2sum method)</a>
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</li>
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<li><a href="PascalX.html#PascalX.xscorer.rsum.score_map">score_map() (PascalX.xscorer.rsum method)</a>
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<ul>
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<li><a href="PascalX.html#PascalX.xscorer.zsum.score_map">(PascalX.xscorer.zsum method)</a>
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</li>
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</ul></li>
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<li><a href="PascalX.html#PascalX.pathway.chi2perm.set_genescorer">set_genescorer() (PascalX.pathway.chi2perm method)</a>
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<h2 id="T">T</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<li><a href="PascalX.html#PascalX.genescorer.chi2sum.test_gene_assocdir">test_gene_assocdir() (PascalX.genescorer.chi2sum method)</a>
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</tr></table>
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<h2 id="W">W</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<li><a href="PascalX.html#PascalX.genescorer.wchi2sum">wchi2sum (class in PascalX.genescorer)</a>
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</li>
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</ul></td>
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<h2 id="Z">Z</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="PascalX.html#PascalX.xscorer.zsum">zsum (class in PascalX.xscorer)</a>
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</li>
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</ul></td>
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</tr></table>
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</div>

‎docs/index.html‎

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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.genome.genome"><code class="docutils literal notranslate"><span class="pre">genome</span></code></a></li>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#genescorer">Genescorer</a></li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#genescorer">Genescorer</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.genescorer.genescorer"><code class="docutils literal notranslate"><span class="pre">genescorer</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.genescorer.chi2sum"><code class="docutils literal notranslate"><span class="pre">chi2sum</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.genescorer.wchi2sum"><code class="docutils literal notranslate"><span class="pre">wchi2sum</span></code></a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#pathwayscorer">Pathwayscorer</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.pathway.chi2rank"><code class="docutils literal notranslate"><span class="pre">chi2rank</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.pathway.chi2perm"><code class="docutils literal notranslate"><span class="pre">chi2perm</span></code></a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#xscorer">Xscorer</a></li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#genexprscorer">Genexprscorer</a></li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#xscorer">Xscorer</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.xscorer.zsum"><code class="docutils literal notranslate"><span class="pre">zsum</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.xscorer.rsum"><code class="docutils literal notranslate"><span class="pre">rsum</span></code></a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#genexprscorer">Genexprscorer</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.genexpr.genexpr"><code class="docutils literal notranslate"><span class="pre">genexpr</span></code></a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="PascalX.html#snp-database">SNP database</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="PascalX.html#PascalX.snpdb.db"><code class="docutils literal notranslate"><span class="pre">db</span></code></a></li>
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</ul>
@@ -166,7 +178,6 @@ <h2>License and citation policy<a class="headerlink" href="#license-and-citation
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<h2>Contact<a class="headerlink" href="#contact" title="Permalink to this heading"></a></h2>
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<ul class="simple">
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<li><p>For all technical issues (bug reports, etc.), please open a ticket on the <a class="reference external" href="https://github.com/BergmannLab/PascalX/issues">GitHub</a> page.</p></li>
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<li><p>For general inquiries, please contact the main contributor: Daniel.Krefl(&#64;unil.ch)</p></li>
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