getterm.gene: get all the term genes under the term "biological process",...

In robert19960424/IndGOterm: Tools for filtrating dysregulation terms from personalized patient

Description

the function can get all the offspring pathway and their entire genes under "biological_process" , "molecular_function" or "cellular_component"

Usage

getterm.gene(
  term,
  gene2go_human,
  graph_path,
  relation = c("biological_process", "molecular_function", "cellular_component")
)

Arguments

term	a matrix or data.frame contains the informations of the terms in the Gene Ontology database. Download from http://archive.geneontology.org/lite/2019-07-06/. By default the variables are taken from environment(formula).
gene2go_human	a matrix or data.frame contains the informations of the geneID matching to the GOID. Download from https://ftp.ncbi.nih.gov/gene/DATA/ and should be preprocessed to get the matrix or data.frame of geneID matching to GOID of human beings. By default the variables are taken from environment(formula).
graph_path	a matrix or data.frame contains the informations of relations of parent term and son term. Doownload from http://archive.geneontology.org/lite/2019-07-06/. By default the variables are taken from environment(formula).
relation	a character string specifying the research direction , must be one of "biological_process","molecular_function" or "cellular_component"

Value

a matrix whose row is geneID and col is termID

Examples

term_gene<-getterm.gene<-function(term,gene2go_human,graph_path,relation="biological_process")

robert19960424/IndGOterm documentation built on Feb. 9, 2021, 8:37 a.m.