Can'T Run Properly The Getlds Function In Biomart Package.
Hello, every body I want to do a mapping from uniportIDs to Ensemble gene IDs using biomaRt package in R I have used the followed instruction
library(biomaRt)
ensemble<-useMart("ensembl",dataset="scerevisiae_gene_ensembl")
mart2 <-useMart("ensembl",dataset="protein")
proteins<-c("P53736","P53737","P53738","P53739","P53740","P53741","P53742","P53743","P53744","P53745")
getLDS(attributes="ensembl_gene_id",mart=ensemble,attributesL="protein_accession",filtersL="protein_accession",valuesL=proteins,martL=mart2)
I get the following error:
Error in get(filtersL, env = martFilters(martL)) : invalid 'envir' argument
Do someone have an idea about it? Thank you.
1 answer
I have not used the getLDS() function, but I think the problem is that protein_accession is not a valid attribute. You can get all of the attributes into a data frame using the listAttributes() function:
library(biomaRt)
attrs <- listAttributes(ensemble)
It looks like you have UniProt protein IDs, so you can look for attributes named "uniprot" using grep:
attrs[grep("uniprot", attrs$name),]
name description
44 uniprot_sptrembl UniProt/TrEMBL Accession
45 uniprot_swissprot UniProt/SwissProt ID
46 uniprot_swissprot_accession UniProt/SwissProt Accession
Then, I would use getBM() to retrieve the gene IDs:
results <- getBM(attributes = c("ensembl_gene_id", "uniprot_swissprot_accession"),
filters = "uniprot_swissprot_accession", values = proteins, mart = ensemble)
results
ensembl_gene_id uniprot_swissprot_accession
1 YNR040W P53736
2 YNR042W P53737
3 YNR046W P53738
4 YNR047W P53739
5 YNR048W P53740
6 YNR051C P53741
7 YNR053C P53742
8 YNR054C P53743
9 YNR056C P53744
10 YNR059W P53745
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