seq2pathway (version 1.4.0)

FisherTest_MsigDB: A wrapper function to perform conditional Fisher's exact test, using custom-defined genesets.

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

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)