enrichKEGGPathway: KEGG pathway enrichment tests. 'enrichKEGGPathway' will do...

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

Usage

enrichKEGGPathway(entrez.gene.list, pathway.list = NA,
  whole.gene.number = 22333, threshold = 0.05, adjust.p.method = "BH",
  organism = "hsa")

Arguments

entrez.gene.list	character vector, entrez gene IDs of DE genes.,
pathway.list	character vector, KEGG pathway IDs. If NA, the function will use all the pathways in KEGG website 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.
organism	character, 3 characters' KEGG organism code, default hsa (human).

Details

enrichKEGGPathway is used for pathway enrichment. The pathway information is fetched from KEGG website. phyper is used to do the hypergeometric tests. p.adjust is used to calculate the p adjustes.

Value

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

See Also

viewKEGGPathwayInfo p.adjust phyper

Examples

data("deg")

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

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

enrich.result

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