FisherTest_GO_BP_MF_CC: A wrapper function to perform the Fisher's exact test, using...

In xyang2uchicago/seq2pathway: a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Description

A wrapper function to perform the Fisher's exact test, using GO-defined genesets.

Usage

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)

Arguments

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.

Value

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

Author(s)

Bin Wang, Xinan Yang

Examples

  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)          

xyang2uchicago/seq2pathway documentation built on Dec. 23, 2021, 7:14 p.m.