term_enrichment: term_enrichment

In MTZimmer/RITAN: Rapid Integration of Term Annotation and Network resources

Description

term_enrichment evaluates the input gene list for enrichment within each of the annotation resources. This differs from the enrichment_symbols function which evaluates the gene list for enrichment against all of the annotation resources grouped together.

Usage

term_enrichment(geneset, resources = resources.default,
  report_resources_separately = FALSE, verbose = TRUE, all_symbols = NA,
  filter_to_intersection = FALSE, ...)

Arguments

geneset	vector of gene symbols to be evaluated
resources	list containing the reference gene sets to test for enrichment
report_resources_separately	logical (default FALSE) flag to report enrichments seperately for each requested resource, or to combine them and produce FDR adjustment across the combined set
verbose	print the top results for each annotation resource
all_symbols	the background/global set of gene symbols (study dependent; we provide all protien coding genes as a default)
filter_to_intersection	[FALSE] should the background and foreground genesets be subsetted to one another?
...	further arguments are passed on to enrichment_symbols()

Value

results matrix of input gene list compared to active gene sets. Q value is calculated within each of the active gene sets.

Examples

## Check if there is enrichment for any "Hallmark" functions within a input set of genes
require(RITANdata)
myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5')
e <- term_enrichment(myGeneSet, "MSigDB_Hallmarks")
print( e[1:2, -6] )

## Not run: 
term_enrichment(geneset = vac1.day0vs31.de.genes)
term_enrichment(geneset = vac1.day0vs31.de.genes, resources = "MSigDB_Hallmarks")
vac1.day0v31.enrichment <- term_enrichment(geneset = vac1.day0vs31.de.genes, verbose = FALSE)

## End(Not run)

MTZimmer/RITAN documentation built on Feb. 21, 2020, 7:09 a.m.