transToTSS:
A data frame with Ensemble transcript IDs and transcriptional start sites.
Description
The data frame stores Ensemble transcript IDs and repective chromosomes,
transcriptional start sites and strands for mus musculus (mm10).
Usage
data(transToTSS)
Arguments
Format
A data frame with 277 mouse transcripts with the following 4 variables:
ensembl_transcript_id
A character giving the Ensemble
transcript ID.
chromosome_name
A character with the respective
chromomse name.
transcript_start
An integer storing the respective
transcriptional start site.
strand
An integer storing the respective strand
information.
Source
http://www.ensembl.org
Details
Given a character vector transcripts with the Ensemble
transcript IDs, a data frame like this can be obtained via biomaRt:
library("biomaRt")
mart <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
transToTSS <- getBM(attributes=c("ensembl_transcript_id",
"chromosome_name", "transcript_start", "transcript_end", "strand"),
filters="ensembl_transcript_id", values=transcripts, mart=mart)