setup_genesets {chipenrich}R Documentation

Function to setup genesets

Description

Function to setup genesets

Usage

setup_genesets(gs_codes, ldef_obj, genome, min_geneset_size, max_geneset_size)

Arguments

gs_codes

A character vector of geneset databases to be tested for enrichment. See supported_genesets(). Alternately, a file path to a a tab-delimited text file with header and first column being the geneset ID or name, and the second column being Entrez Gene IDs.

ldef_obj

A LocusDefinition object to use for filtering gene sets based on which genes are defined in the locus defintion.

genome

One of the supported_genomes().

min_geneset_size

Sets the minimum number of genes a gene set may have to be considered for enrichment testing.

max_geneset_size

Sets the maximum number of genes a gene set may have to be considered for enrichment testing.

Value

A list with components consisting of GeneSet objects for each of the elements of genesets. NOTE: Custom genesets must be run separately from built in gene sets.


[Package chipenrich version 2.18.0 Index]