filter_genesets {chipenrich}R Documentation

Function to filter genesets by locus definition and size

Description

This function filters gene sets based on the genes that are present in a particular locus definition. After determining which genes are present in both the GeneSet, gs_obj, and the LocusDefinition ldef_obj, gene sets are filtered by size with min_geneset_size and max_geneset_size.

Usage

filter_genesets(
  gs_obj,
  ldef_obj,
  min_geneset_size = 15,
  max_geneset_size = 2000
)

Arguments

gs_obj

A valid GeneSet object

ldef_obj

A valid LocusDefinition object

min_geneset_size

An integer indicating the floor for genes in a geneset. Default 15.

max_geneset_size

An integer indicating the ceiling for genes in a geneset. Default 2000.

Value

An altered gs_obj with changed set.gene and all.genes slots reflecting min_geneset_size and max_geneset_size after intersecting with the genes present in the particular locus definition.


[Package chipenrich version 2.17.0 Index]