score_geneset_oddsratio

gs_signif = number of significant genes in geneset G that intersect with user's genelist (i.e. foreground genes in G)
gs_all = number of genes in geneset G that intersect with user's genelist (i.e. foreground+background genes in G)
k_signif = total number of significant genes in user's genelist
k_all = total number of genes in user's genelist
gs_signif/gs_all = ratio of foreground genes in geneset G
k_signif/k_all = ratio of overall foreground genes (i.e. expected value for a random geneset)
oddsratio = (gs_signif/gs_all) / (k_signif/k_all)

Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

Frank Koopmans

goat

Gene Set Analysis Using the Gene Set Ordinal Association Test

score_geneset_oddsratio function

<dl><dt>genesets</dt>
<dd>tibble with genesets, must contain columns 'source', 'id', 'ngenes', 'ngenes_signif'</dd>
<dt>genelist</dt>
<dd>tibble with genes, must contain columns 'gene', 'signif'</dd></dl>

Arguments

Compute odds-ratio for each geneset — score_geneset_oddsratio

<dl>

<dt>genesets</dt>
<dd>tibble with genesets, must contain columns 'source', 'id', 'ngenes', 'ngenes_signif'</dd>


<dt>genelist</dt>
<dd>tibble with genes, must contain columns 'gene', 'signif'</dd>

</dl>

score_geneset_oddsratio: Compute odds-ratio for each geneset

Description

Usage

Value

Arguments