I am trying to make the org.db (x) argument in AnnotationDbi::mapIds() as variable, But
genelist <- c("ENSG00000074800","ENSG00000116285","ENSG00000171603","ENSG00000049245")
org_pkg <- "org.Hs.eg.db"
library(AnnotationDbi)
library(org_pkg)
entrez_Ids <- mapIds(org_pkg, as.character(genelist), 'ENTREZID', 'ENSEMBL')
Getting an Error message:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘mapIds’ for signature ‘"character"’
Tried with as.symbol(org_pkg) But no help.
•
written
by
sangram_keshari
You are not loading your packages correctly. org_pkg is a string (i.e. class character).
Try this instead:
library(AnnotationDbi)
library(org.Hs.eg.db)
genelist <- c("ENSG00000074800","ENSG00000116285","ENSG00000171603","ENSG00000049245")
org_pkg <- org.Hs.eg.db
entrez_Ids <- mapIds(org_pkg, as.character(genelist), 'ENTREZID', 'ENSEMBL')
Resulting in:
head(entrez_Ids)
ENSG00000074800 ENSG00000116285 ENSG00000171603 ENSG00000049245
"2023" "54206" "22883" "9341"
EDIT: Another simpler fix
genelist <- c("ENSG00000074800","ENSG00000116285","ENSG00000171603","ENSG00000049245")
org_pkg <- "org.Hs.eg.db"
library(AnnotationDbi)
library(org_pkg,character.only=TRUE)
entrez_Ids <- mapIds(eval(parse(text = org_pkg)), as.character(genelist), 'ENTREZID', 'ENSEMBL')
Thanks for the answer. Yes this gives an output.
But suppose I am receiving a string object in org_pkg (because its coming from an Rscript argument, and its always a string). Then how to convert that string object to an AnnotationDbi class.
Good question!
library(org_pkg,character.only=TRUE)
I have no problem with loading package if the org_pkg is a string, Problem comes with mapIds()
entrez_Ids <- mapIds(eval(parse(text = org_pkg)), as.character(genelist), 'ENTREZID', 'ENSEMBL')
Hey thank you so much. It solved :)
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