Problem with biomarRt's getSequence() function
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vsn ▴ 10
@vsn-14314
Last seen 3.9 years ago
USA

Hello!

I am new to Bioconductor and I am experiencing an error while using getSequence() in biomart.

The code is given below:

library("biomaRt")
ensemblp <- useMart(biomart="plants_mart",host="plants.ensembl.org")
osj = useDataset("osativa_eg_gene", mart = ensemblp)
genes <- read.csv("osj.csv")
osj_id <- genes$ensembl_transcript_id

os_genes <- getSequence(id = osj_id, type = "ensembl_transcript_id", seqType = "peptide", mart = ensemblp)

show(os_genes)

 

Error message:

Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : 
  This function only works when used with the ensembl BioMart.This function only works when used with the ENSEMBL_MART_ENSEMBL BioMart.
 

Did I make any mistake in code? Please help me fix the error. 

Thanks!

biomart error plants_mart getSequence • 699 views
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