gage.enrich: gage Geneset Enrichment Test

In christensensm/COMPOSE: Calculation and Visualization of Phenotypic CRISPR Screens

Description

gage.enrich utilizes the package 'gage' to test for enrichment of user-input gene sets

Usage

gage.enrich(
  CSS,
  geneset,
  genome.db = org.Hs.eg.db,
  gene.ids = "SYMBOL",
  species = "hsa",
  database = NULL
)

Arguments

CSS	output CRISPR screen score matrix from create.CSS()
geneset	input geneset
genome.db	genome database from which to convert gene symbols to entrez ids
gene.ids	type of gene ids in the geneset. Options are currently either 'symbol' or 'entrez'
species	species for pathview (if KEGG genesets are used)
database	for visualizing pathways (use only if your database is KEGG)

Value

list of output from gage

See Also

gage, pathview

Examples

enriched.kegg <- gage.enrich(results$CSS, kegg.genesets, gene.ids = 'entrez',
species = 'hsa', kegg = T)
enriched.msigdb <- gage.enrich(results$CSS, c2.canonical, gene.ids = 'symbol')
...

christensensm/COMPOSE documentation built on Dec. 22, 2020, 3:43 a.m.