fgsea.enrich: FGSEA utility

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

Description

fgsea.enrich utilizes the package 'fgsea' to test for enrichment of user-given genesets in your gene list

Usage

fgsea.enrich(
  CSS,
  geneset,
  genome.db = Org.Hs.eg.db,
  gene.ids = "SYMBOL",
  p.value = 0.05,
  minSize = 15,
  maxSize = 500,
  nperm = 10000,
  top = 10,
  collapsepath = FALSE
)

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'
p.value	specified cutoff for pathway significance
minSize	low cutoff for fgsea gene set size
maxSize	high cutoff for fgsea gene set size
nperm	number of permutations for fgsea analysis
top	number of top pathways to display
collapsepath	logical: collapse pathways using fgsea's collapsePathways function

Value

object of fgsea output

See Also

fgsea

Examples

fgsea.enrich <- reactomepa.enrich(CSS.data[,2, drop=FALSE])
fgsea.enrich <- reactomepa.enrich(CSS.data[,c(2:4)])
...

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