PathAnalysis: Main Function for pathway analysis.

In metaOmic/MetaDE: MetaDE: Transcriptome meta-analysis for differentially expressed gene detection

Description

Main Function for pathway analysis The PathAnalysis is a function to perform pathway analysis (a.k.a. gene set enrichment test) for functional annotation of a candidate gene list or an ordered gene result from Meta DE analysis output.

Usage

PathAnalysis(meta.p = NULL, pathway = c(Biocarta.genesets, GOBP.genesets,
  GOCC.genesets, GOMF.genesets, KEGG.genesets, Reactome.genesets),
  enrichment = c("KS", "Fisher's exact"), p.cut = NULL,
  DEgene.number = 200, size.min = 15, size.max = 500)

Arguments

meta.p	is a vector of meta-analysis p-value.
pathway	is a vector of pathway databases used for functional analysis, see data(pathways) for more details.
enrichment	is the method used for pathway analysis, must be one of "KS" and "Fisher's exact".
p.cut	is the p-value cutoff to select the DE genes, option for Fisher's exact method only.
DEgene.number	is the top number of DE genes, option for Fisher's exact method only.
size.min	is the minimum pathway size to be included in the functional analysis.
size.max	is the maximum pathway size to be included in the functional analysis.

Value

a data frame with columns:

• pvalue the p-value from pathway analysis for each pathway

• qvalue the q-value from pathway analysis for each pathway

• OddsRatio optional, the odds ratio from Fisher's exact test method

• logOR optional, the log odds ratio from Fisher's exact test method

• DEgenes optional, the set of DE genes in each pathway

Examples

## Not run: 
meta.p  <- meta.res$meta.analysis$pval
ks.result <- PathAnalysis(meta.p = meta.p, enrichment = "KS")
fisher.result <- PathAnalysis(meta.p = meta.p, enrichment = "Fisher's exact")

## End(Not run)

metaOmic/MetaDE documentation built on May 22, 2019, 6:54 p.m.