Help for package toprdata

Title:

Gene and Exon Data from Ensembl

Version:

1.0.2

Description:

Gene and exon information from Ensembl genome builds GRCh38.p13 (104) and GRCh37 (v40) to use with the 'topr' package.

License:

LGPL (≥ 3)

Encoding:

UTF-8

LazyData:

true

LazyDataCompression:

RoxygenNote:

7.2.0

Suggests:

testthat (≥ 3.0.0), knitr, rmarkdown, markdown

Config/testthat/edition:

Depends:

R (≥ 3.5.0)

NeedsCompilation:

Packaged:

2023-02-10 10:56:27 UTC; thorhildur

Author:

Thorhildur Juliusdottir [cph, aut, cre], Andri Stefansson [aut]

Maintainer:

Thorhildur Juliusdottir <totajuliusd@gmail.com>

Repository:

CRAN

Date/Publication:

2023-02-10 12:00:02 UTC

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)