FisherTest_MsigDB: A wrapper function to perform conditional Fisher's exact...

In seq2pathway: a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Description

A wrapper function to perform conditional FET, using custom-defined genesets.

Usage

FisherTest_MsigDB(gsmap, gs, genome=c("hg38","hg19","mm10","mm9"), 
                  min_Intersect_Count=5)

Arguments

gsmap	An R GSA.genesets object defined by the package "GSA" for functional gene-set (or termed as pathway for simplification). User can call the GSA.read.gmt function in R GSA package to load customized gene-sets with a .gmt format.
gs	A characteristic vector of gene symbols, the input genelist.
genome	A character specifies the genome type. Currently, choice of "hg38", "hg19", "mm10", and "mm9" is supported.
min_Intersect_Count	A number decides the cutoff of the minimum number of intersected genes when reporting Fisher's exact tested results.

Value

A data frame of Fisher's exact tested result with the following columns:

GeneSet	MSigDB gene-set names (IDs)
Description	MSigDB definition and description for gene-sets
Fisher_Pvalue	the raw Pvalues
Fisher_odds	estimate of the odds ratios
FDR	the multi-test adjusted Pvalues using the Benjamini and Hochberg method
Intersect_Count	the sizes of the overlap between the MSigDB gene-set genes and the input genelist
MsigDB_gene_inBackground	the counts of genes among each MSigDB gene-set that are also within genome background
MsigDB_gene_raw_Count	the original counts of genes in each MSigDB gene-set
Intersect_gene	the intersecting genes' symbols

Author(s)

Bin Wang

Examples

  data(dat_chip)
  data(MsigDB_C5,package="seq2pathway.data")
  #generate a demo GSA.genesets object
  demoDB <- MsigDB_C5
  x=100
  for(i in 1:3) demoDB[[i]]<-MsigDB_C5[[i]][1:x]
  FS_test<-FisherTest_MsigDB(gsmap=demoDB, 
	 sample(unlist(demoDB$genesets),10), genome="hg19",
	 min_Intersect_Count=1)
  FS_test[1:3,]
  ## Not run: 
  FS_test<-FisherTest_MsigDB(gsmap=MsigDB_C5, 
	gs=rownames(dat_chip), genome="hg19", 
	min_Intersect_Count=1)
	
## End(Not run)

seq2pathway documentation built on Nov. 8, 2020, 6:27 p.m.