FisherTest_MsigDB {seq2pathway} | R Documentation

## 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

### 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)

[Package seq2pathway version 1.18.0 Index]