hyperEnrichment: Carry out set enrichment test based on hyper-geometric...

In montilab/BS831: Boston University - Genomics Data Mining

Carry out set enrichment test based on hyper-geometric distribution

Description

Carry out set enrichment test based on hyper-geometric distribution

Usage

hyperEnrichment(
  drawn,
  categories,
  ntotal = length(unique(unlist(categories))),
  min.drawsize = 4,
  mht = TRUE,
  verbose = TRUE
)

Arguments

drawn	One or more sets of 'drawn' items (e.g., genes). Basically, a list of signatures.
categories	list of gene sets (e.g., MSigDB c2)
ntotal	background population, i.e., the total no. of items from which items are supposed to have been drawn
min.drawsize	min no. of drawn items that must be among categories' items
mht	correct for multiple hypothesis testing across multiple 'draws'

Value

a data.frame with rows indexed by the signature(s) tested

Examples

# load objects hyperSig (a list of signatures) and hyperGsets (a GeneSet object)
# and run hyper-enrichment test

data(hyper) # contains objects hyperSig and hyperGsets
hyperE <- hyperEnrichment(drawn=hyperSig,categories=getGeneSet(hyperGsets),ntotal=10000)
head(hyperE)

montilab/BS831 documentation built on April 17, 2024, 4:51 p.m.