enrichMSigDB: MSigDB data sets enrichment tests. 'enrichMSigDB' will do the...

In wolfsonliu/enrich: Gene list enrichment on KEGG pathway, GO term, Transcript Factor Targets and so on.

Usage

enrichMSigDB(entrez.gene.list, msigdb = NA, whole.gene.number = 22333,
  threshold = 0.05, adjust.p.method = "BH")

Arguments

entrez.gene.list	character vector, entrez gene IDs of DE genes.,
msigdb	list of MSigDBSet. If NA, the function will load data MSigDB of the package automatically.
whole.gene.number	numeric, the total backgroud number of all genes.
threshold	numeric, output tests' adjusted p value cut off, default 0.05.
adjust.p.method	character, method used in p.adjust.

Details

enrichMSigDB is used for MSigDB sets enrichment. The sets come from MSigDB web (http://software.broadinstitute.org/gsea/msigdb).

Value

data.frame with columns, Term (MSigDB set names), Type (always MSigDB), ID (MSigDB set SYSTEMATIC_NAME), Input.number (number of input genes in the set), Background.number (number of all genes in the set), P.value, adjusted.P.value.

See Also

enrichKEGGPathway MSigDB MSigDBSet

Examples

data("deg")

de.entrez <- as.character(na.omit(deg$entrezgene))

enrich.result <- enrichMSigDB(
    entrez.gene.list  = de.entrez,
    msigdb            = NA,
    whole.gene.number = 20000,
    threshold         = 0.05,
    adjust.p.method   = "BH"
)

enrich.result

wolfsonliu/enrich documentation built on May 4, 2019, 9:47 a.m.