FisherTest_GO_BP_MF_CC {seq2pathway} | R Documentation |
A wrapper function to perform the Fisher's exact test, using GO-defined genesets.
FisherTest_GO_BP_MF_CC(gs, genome=c("hg38","hg19","mm10","mm9"), min_Intersect_Count=5, Ontology=c("GOterm", "BP","MF", "CC","newOntology"), newOntology=NULL)
gs |
A characteristic vector of gene symbols, the input gene list. |
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. |
Ontology |
A character specifies the Gene Ontology, choice of "GOterm", "BP","MF", "CC" and "newOntology" is supported. |
newOntology |
A list of two lists with the same ontology IDs. or each ontology ID, the 1st list is the lists of defined genes and the 2nd list is the desceiption. |
A list of 3 data frames, each is a result of Fisher's exact test, using GO CC, BP, MF respectively. Each data frame reports FET results with the following columns.
GOID |
GO term IDs |
Description |
GO definition and description for the gene-sets |
Fisher_Pvalue |
is the raw P-values |
Fisher_odds |
estimate of the odds ratios |
FDR |
the multi-test adjusted P-values using the Benjamini and Hochberg method |
Intersect_Count |
the sizes of overlap between GO gene members and the input genelist |
GO_gene_inBackground |
the counts of genes among each GO term that are also within the given genome background |
GO_gene_raw_count |
the original counts of genes in each GO term |
Intersect_gene |
the intersecting genes' symbols |
Bin Wang, Xinan Yang
data(dat_chip) head(dat_chip) data(GO_BP_list,package="seq2pathway.data") data(Des_BP_list,package="seq2pathway.data") newOntology <- list(GO_BP_list[1:200], Des_BP_list[1:200]) # A demo run of this funcion FS_test<- FisherTest_GO_BP_MF_CC(gs=as.vector(rownames(dat_chip)), Ontology="newOntology", newOntology=newOntology) FS_test ## Not run: data(dat_chip) FS_test<-FisherTest_GO_BP_MF_CC(gs=rownames(dat_chip)[1:20], genome="hg19", min_Intersect_Count=1, Ontology="BP") FS_test$GO_BP[1:3,] ## End(Not run)