gene.list

The list to describe the gene-SNP file for <code><a rd-options="" href="/link/ARTP_pathway?package=ARTP&version=2.0.5" data-mini-rdoc="ARTP::ARTP_pathway">ARTP_pathway</a></code>

misc

For calculating gene and pathway p-values using the Adaptive Rank Truncated Product test.

Bill Wheeler

ARTP

Gene and Pathway p-Values Computed using the Adaptive Rank
Truncated Product

gene.list function

The format is a list:<dl class="dl-horizontal">
 <dt>file</dt><dd>Text file containing at least 2 columns, where one column is for the SNPs and
 the other column is for the gene containing the SNP. No default.</dd>
 <dt>delimiter</dt><dd>The delimiter used in <code>file</code>.</dd>
 <dt>gene.var</dt><dd>Variable name or column number of the gene variable. The default is "Gene".</dd>
 <dt>snp.var</dt><dd>Variable name or column number of the SNP variable. The default is "SNP".</dd>
 <dt>chrm.var</dt><dd>Variable name or column number of the chromosome variable. The default is "Chr".
 This option is only used for calling <code><a rd-options="" href="/link/plot_genes?package=ARTP&version=2.0.5" data-mini-rdoc="ARTP::plot_genes">plot_genes</a></code>.</dd>
 <dt>header</dt><dd>0 or 1 to denote if <code>file</code> contains a header of variable names. The default is 1.</dd>
 </dl>

Format

The list to describe the gene-SNP file for <code><a rd-options='' href='ARTP_pathway'>ARTP_pathway</a></code>

List to describe the gene-SNP file — gene.list

The format is a list:<dl class='dl-horizontal'>
 <dt>file</dt><dd>Text file containing at least 2 columns, where one column is for the SNPs and
 the other column is for the gene containing the SNP. No default.</dd>
 <dt>delimiter</dt><dd>The delimiter used in <code>file</code>.</dd>
 <dt>gene.var</dt><dd>Variable name or column number of the gene variable. The default is "Gene".</dd>
 <dt>snp.var</dt><dd>Variable name or column number of the SNP variable. The default is "SNP".</dd>
 <dt>chrm.var</dt><dd>Variable name or column number of the chromosome variable. The default is "Chr".
 This option is only used for calling <code><a rd-options='' href='plot_genes'>plot_genes</a></code>.</dd>
 <dt>header</dt><dd>0 or 1 to denote if <code>file</code> contains a header of variable names. The default is 1.</dd>
 </dl>

gene.list: List to describe the gene-SNP file

Description

Arguments

Format

Details