Description Usage Arguments Value Examples
the function can get all the offspring pathway and their entire genes under "biological_process" , "molecular_function" or "cellular_component"
1 2 3 4 5 6 | getterm.gene(
term,
gene2go_human,
graph_path,
relation = c("biological_process", "molecular_function", "cellular_component")
)
|
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" |
a matrix whose row is geneID and col is termID
1 | term_gene<-getterm.gene<-function(term,gene2go_human,graph_path,relation="biological_process")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.