Package 'toprdata'

Title: Gene and Exon Data from Ensembl
Description: Gene and exon information from Ensembl genome builds GRCh38.p13 (104) and GRCh37 (v40) to use with the 'topr' package.
Authors: Thorhildur Juliusdottir [cph, aut, cre], Andri Stefansson [aut]
Maintainer: Thorhildur Juliusdottir <[email protected]>
License: LGPL (>= 3)
Version: 1.0.2
Built: 2025-02-28 05:47:54 UTC
Source: https://github.com/cran/toprdata

Help Index

Ensembl exons build HG38-104-5-2

Description

https://www.ensembl.info/2021/05/05/ensembl-104-has-been-released/

Usage

ENSEXONS

Format

A data frame with 40,122 rows and 7 variables:

chrom

Chromosome on build version 38 (GRCh38/hg38)

gene_start

genetic position of gene start on build version 38

gene_end

genetic position of gene end on build version 38

gene_symbol

The name of the gene

exon_chromstart

genetic positions of exon start

exon_chromend

genetic position of exon end

Details

exons on chrY and chrM were excluded from the exon dataset

Ensembl exons build HG37 (GRCh37) v40 from gencode

Description

exons on chrY and chrM were excluded from the exon dataset

Usage

ENSEXONS_37

Format

A data frame with 62,739 rows and 7 variables:

chrom

Chromosome on build version 38 (GRCh38/hg38)

gene_start

genetic position of gene start on build version 38

gene_end

genetic position of gene end on build version 38

gene_symbol

The name of the gene

exon_chromstart

genetic positions of exon start

exon_chromend

genetic position of exon end

Ensembl genes build HG38.104-5-2

Description

https://www.ensembl.info/2021/05/05/ensembl-104-has-been-released/

Usage

ENSGENES

Format

A data frame with 40,122 rows and 5 variables:

chrom

Chromosome on build version 38 (GRCh38/hg38)

gene_start

genetic position of gene start on build version 38

gene_end

genetic position of gene end on build version 38

gene_symbol

The name of the gene

biotype

the biotype of the gene

Details

genes on chrY and chrM were excluded

Ensembl genes build HG37 (GRCh37) v40 from gencode

Description

genes on chrY and chrM were excluded

Usage

ENSGENES_37

Format

A data frame with 62,743 rows and 5 variables:

chrom

Chromosome on build version 38 (GRCh38/hg38)

gene_start

genetic position of gene start on build version 38

gene_end

genetic position of gene end on build version 38

gene_symbol

The name of the gene

biotype

the biotype of the gene

toprdata

Description

Gene and exon datasets to use with the 'topr' package

datasets

The two datasets are:

  • ENSGENES Gene information from genome build GRCh38

  • ENSEXONS Exon information from genome build GRCh38

  • ENSGENES_37 Gene information from genome build GRCh37

  • ENSEXONS_37 Exon information from genome build GRCh37

Examples

library(toprdata)
head(ENSGENES)
head(ENSEXONS)