annotate_signatures_with_genesets: Signatures annotation with gene sets

In greenelab/ADAGEpath: ADAGE-based Signature Analysis

Signatures annotation with gene sets

Description

Annotate signatures with known GO or KEGG gene sets downloaded from the Tribe webserver. Annotation is done through a gene set enrichment test (fisher exact test) with FDR correcting the number of gene sets tested for each signature.

Usage

annotate_signatures_with_genesets(selected_signatures, model, genesets,
  significance_cutoff = 0.05)

Arguments

selected_signatures	a character vector storing names of signatures
model	an ADAGE model to extract signatures from
genesets	a named list of gene sets returned by the function fetch_geneset(), each element in the list is a character vector storing genes (PAO1 locus tag) in a gene set.
significance_cutoff	numeric, FDR significance cutoff used to filter gene sets (default: 0.05).

Value

a data.frame storing significantly enriched gene sets for the input signatures.

greenelab/ADAGEpath documentation built on May 25, 2022, 7:11 a.m.