I want to extract genes which have GO of "anatomical structure development" or its subcategory GOs.
I found there is "with_go" or "go" in the list of available filters and I am wondering what is "with_go"?
I tried
library(biomaRt)
db <- useMart("ensembl")
hg <- useDataset("hsapiens_gene_ensembl", mart = db)
res <- getBM(attributes = c("ensembl_gene_id", "go_id", "name_1006"),
filters = c("ensembl_gene_id_version","with_go"),
values = list(genelist,"GO:0048856"=TRUE),
mart = hg)
or
library(biomaRt)
db <- useMart("ensembl")
hg <- useDataset("hsapiens_gene_ensembl", mart = db)
res <- getBM(attributes = c("ensembl_gene_id", "go_id", "name_1006"),
filters = c("ensembl_gene_id_version","go"),
values = list(genelist,"GO:0048856"),
mart = hg)
and I have got much more genes from "with_go". Does it retrieve all the genes with the GO and its subcategory?
Thank you
Rio