FisherTest_MsigDB {seq2pathway} | R Documentation |
A wrapper function to perform conditional FET, using custom-defined genesets.
FisherTest_MsigDB(gsmap, gs, genome=c("hg38","hg19","mm10","mm9"), min_Intersect_Count=5)
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. |
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 |
Bin Wang
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)