transToTSS: A data frame with Ensemble transcript IDs and transcriptional...

In epigenomix: Epigenetic and gene transcription data normalization and integration with mixture models

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)

epigenomix documentation built on Nov. 8, 2020, 5:24 p.m.