Search
Question: Problem with biomarRt's getSequence() function
1
gravatar for vsn
20 days ago by
vsn10
USA
vsn10 wrote:

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!

ADD COMMENTlink written 20 days ago by vsn10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 154 users visited in the last hour