enrichmentGSEA: Performing GSEA analysis with the fgsea package

In uc-bd2k/CLEAN: Clustering Enrichment Analysis

Performing GSEA analysis with the fgsea package

Description

This function uses the GSEA methodology to perform enrichment analysis of transciptional signatures. The statistical significance is calculated by random gene permutations.

Usage

enrichmentGSEA(sigvals,geneids,diffexp=NULL, functionalCategories=c("KEGG","GO","tfacts","dorotheatfs","hallmark"), directions=c("both"),species="Hs", excel=F,sigFDR=0.1,nperm=100000)

Arguments

sigvals	A vector of p-values, same length and order as "geneids".
geneids	A vector of Entrez gene IDs, may contain duplicates and missing values.
diffexp	log2 differential expression levels.
functionalCategories	Functional categories to be tested- currently, options include "GO", "KEGG" and various other categories, default = "GO". Can be provided by function getFunctionalCategories().
directions	Specifies which of the directions are changes is used in the enrichment values can be "both" (default), "up", "down" and the combinations of the three.
species	Species to further specify database, human="Hs", mouse="Mm", rat="Rn", etc. Default ="Hs".
excel	Specifies whether the results should be organize in excell sheets. Default is FALSE. If results are big it can cause Java issues.
sigFDR	Categories with FDR <= sigFDR will be returned. If NULL it is set to 1.
nperm	Number of random gene samples used for calculating p-values.

Details

This function uses the GSEA methodology as implemented in the fgsea package to perform enrichment analysis of transciptional signatures. The statistical significance is calculated by random gene permutations.

Value

Object is a list of lists of dataframes for each of the functional categories used in the analysis. For functional category a list of dataframes of results corresponding to directions (both, up, down) specified is generated.

Author(s)

Mario Medvedovic

See Also

CLEAN.Hs, fgsea

Examples

data(cMap)
de<-rnorm(11911)
res <- enrichmentGSEA(sigvals=cMap$cMapPvalues[,2],diffexp=de, geneids=cMap$cMapPvalues[,1], functionalCategories=c("KEGG","tfacts"), species="Hs",sigFDR=.5,nperm=10000)
names(res)
names(res$both)
head(res$both$KEGG)

uc-bd2k/CLEAN documentation built on Sept. 22, 2022, 4:12 a.m.