hypergeoTestForGeneset: Hypergeometric test for gmt style list

In LittleHeronCodes/Lazy2: Lazy Package

Hypergeometric test for gmt style list

Description

Gene list hypergeometric test against gmt format list of gene set. Can be used for custom pathway analysis or CMAP style query.

Usage

hypergeoTestForGeneset(query, refGMT, gspace, minGeneSet = 10, ef.psc = 0)

hypergeoTestForGeneset2(
  query,
  refGMT,
  gspace,
  minGeneSet = 10,
  ncore = 1,
  ef.psc = 0
)

Arguments

query	gene set to query (eg. Differentially Expressed Genes)
refGMT	list of reference gene set (eg. Pathways)
gspace	background gene space. Should contain all genes in query.
minGeneSet	minimum size of gene set. This is used to filter refGMT. Default 10
ef.psc	pseudocount when calculating enrichment factor (oddsRatio). Default 0
ncore	number of cores used in hypergeoTestForGeneset2 (soon to be removed)

Value

Data frame of gene set analysis results

pVal

: hypergeometric test p values from phyper

logP

: -log10(p value)

oddsRatio

: odds ratio

tanco

: tanimoto coefficient (Jaccard index)

int

: intersected item count

gsRatio

: gene set ratio (selected genes in gene set / selected genes)

bgRatio

: background ratio (total genes in gene set / total gene space)

Functions

• hypergeoTestForGeneset2(): Using multiprocessing (Deprecated)

Examples

gset <- c("A", "B", "C")
glist <- list(ID1 = LETTERS[1:10], ID2 = LETTERS[4:25])
hypergeoTestForGeneset(gset, glist, LETTERS)

LittleHeronCodes/Lazy2 documentation built on April 20, 2024, 11:24 p.m.