transToTSS {epigenomix} | R Documentation

## 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)

### 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.

### 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)`

### Source

http://www.ensembl.org

### Examples

    data(transToTSS)
    head(transToTSS)

[Package epigenomix version 1.27.1 Index]