I am mapping Entrez gene ids to ensembl ids using biomaRt.
library("biomaRt")
library("readxl")
tbl <- read_excel(input_excel)
tbl <- tbl["EntrezID"]
print(tbl, n=Inf)
listMarts()
ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
filters = listFilters(ensembl)
entrezgene = tbl
genes <- getBM(
filters="entrezgene_id",
attributes=c("ensembl_gene_id","entrezgene_id"),
values=entrezgene,
mart=ensembl)
print(genes)
The input is read from the excel here from this study.
I get the following error message
Error in `[[<-.data.frame`(`*tmp*`, vIdx, value = c("26155", "9636", "375790", : replacement has 494 rows, data has 6909
Calls: getBM ... .generateFilterXML -> .splitValues -> [[<- -> [[<-.data.frame
Execution halted
Error in `[[<-.data.frame`(`*tmp*`, vIdx, value = c("26155", "9636", "375790", : replacement has 494 rows, data has 6909
Calls: getBM ... .generateFilterXML -> .splitValues -> [[<- -> [[<-.data.frame
Execution halted
Does 494 rows, data has 6909 this mean only ensembl ids of 494 entrez genes(out of 6909) were mapped?
Could someone look into this? I'm not sure how to resolve this error.
•
written
by
Natasha •
1 answer
The fundamental issue here is that your entrezgene object is a tibble with one column, where as the getBM() function expects to be passed a vector. The internal code doesn't handle this very well and throws the error you saw.
When you run tbl <- mapply(tbl, FUN=as.numeric) you get back a matrix with a single column, which still isn't what the function expects, but it seems to handle it better. However it is not required to provide the IDs as numbers (in fact they will be converted back to characters inside getBM() anyway).
The better solution is to just select the appropriate column from your tbl an return it as a vector, which you could do via: entrezgene <- tbl$EntrezID
I will update biomaRt to check it's being given the correct type of input, and provide some guidance if that's not the case.
Log in to answer this question.
-
Convert Human to Mouse Symbols
written by cthangav •
-
Error when using compareCluster from enichment
written by jacob •
-
Error while converting Gene ID to Ensembl IDs
written by kai_bio •
-
error relate to R
written by rheab1230 •
-
Converting Ensembl gene IDs to Entrez IDs for indexing gene set collections for doing "Ensemble of …
written by Farah
-
Error in using ParsSNP
written by arsala521 •
Can you post the actual function that gives the error? Where is your
getBM()call?Sorry, there was a formatting error. Now it's displayed
Maybe try convert entrez_id from character to nemuric?
Thank you. I added
tbl <- mapply(tbl, FUN=as.numeric)before listMart(). The query proceeds without any error. However, I obtain 7720 entries, whereas my input has 6909 entries.This is normal, many ENTREZ ID map to multiple ENSEMBL ID.