diff --git a/DESCRIPTION b/DESCRIPTION index 08ecc70..dcdc7a4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,26 +1,26 @@ Package: toprdata Title: Gene and Exon Data from Ensembl -Version: 1.0.0 +Version: 1.0.1 Authors@R: c( person("Genuity", "Science", role = "cph", email = "thorhildur@genuitysci.com"), person("Thorhildur", "Juliusdottir", role = c("aut", "cre"),email = "thorhildur@genuitysci.com"), person("Andri", "Stefansson", role = "aut", email = "andri@genuitysci.com") ) -Description: Gene and exon information from Ensembl (build GRCh38.p13) to use with the topr package. +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: xz -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.0 Suggests: testthat (>= 3.0.0), knitr, rmarkdown, markdown Config/testthat/edition: 3 Imports: Depends: R (>= 3.5.0) NeedsCompilation: no -Packaged: 2022-01-07 18:28:24 UTC; thorhildur +Packaged: 2022-08-19 13:12:35 UTC; thorhildur Author: Genuity Science [cph], Thorhildur Juliusdottir [aut, cre], Andri Stefansson [aut] Maintainer: Thorhildur Juliusdottir Repository: CRAN -Date/Publication: 2022-01-10 10:40:02 UTC +Date/Publication: 2022-08-19 13:40:02 UTC diff --git a/MD5 b/MD5 index c4b9215..a3af183 100644 --- a/MD5 +++ b/MD5 @@ -1,10 +1,14 @@ -af3e1c9ea4c23587586d1239265feaa3 *DESCRIPTION +72915b5e421a5bf82922616719449d24 *DESCRIPTION dc21c19f0d6968ee25d441b2cf46017d *NAMESPACE -a2b03d6abe02b0f6d4e3df468d09f11c *NEWS.md -51bf89d39eec3fcd28ba28e8e7fc178d *R/data.R -439627db59c0f7fe26eb175812b3c9e8 *R/toprdata.R +27de19970ae05b22b5b4f6ba3208de29 *NEWS.md +c55ac7e916a0ba72ebccd8ca87032146 *R/data.R +24dcefaeee7cb781eded041183cf5208 *R/toprdata.R 5b48700a4727930888ec284764a056a4 *data/ENSEXONS.rda +ed7949f10b6619857a733efe40f9b024 *data/ENSEXONS_37.rda f82238a6b7c2f8436b97b216f1b749ed *data/ENSGENES.rda +5252a48dff176084a97634c7621ac2ec *data/ENSGENES_37.rda 2120cd03c04db48a7e2c33ab2b389362 *man/ENSEXONS.Rd +093d0ef8c33dd37f33b25e57fc41750a *man/ENSEXONS_37.Rd 6dd44b6aa32491b585052b301cb6df53 *man/ENSGENES.Rd -7da6b0c0c3f2291516b32590d14b9502 *man/toprdata.Rd +5a68aab852111f8ae1b108b12d1c19a4 *man/ENSGENES_37.Rd +f733725a4ab305f6b7328c21f95e08bf *man/toprdata.Rd diff --git a/NEWS.md b/NEWS.md index 87b8490..7a37955 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +# 1.0.1 +* Genome build GRCh37 (v40) from gencode included + # 1.0.0 * First version submitted to CRAN diff --git a/R/data.R b/R/data.R index 9ede063..feeab61 100644 --- a/R/data.R +++ b/R/data.R @@ -31,3 +31,35 @@ #' \item{exon_chromend}{genetic position of exon end} #' } "ENSEXONS" + +#' Ensembl genes build HG37 (GRCh37) v40 from gencode +#' +#' genes on chrY and chrM were excluded +#' +#' @format A data frame with 62,743 rows and 5 variables: +#' \describe{ +#' \item{chrom}{Chromosome on build version 38 (GRCh38/hg38)} +#' \item{gene_start}{genetic position of gene start on build version 38} +#' \item{gene_end}{genetic position of gene end on build version 38 } +#' \item{gene_symbol}{The name of the gene} +#' \item{biotype}{the biotype of the gene} +#' } +"ENSGENES_37" + + +#' Ensembl exons build HG37 (GRCh37) v40 from gencode +#' +#' exons on chrY and chrM were excluded from the exon dataset +#' +#' @format A data frame with 62,739 rows and 7 variables: +#' \describe{ +#' \item{chrom}{Chromosome on build version 38 (GRCh38/hg38)} +#' \item{gene_start}{genetic position of gene start on build version 38} +#' \item{gene_end}{genetic position of gene end on build version 38 } +#' \item{gene_symbol}{The name of the gene} +#' \item{exon_chromstart}{genetic positions of exon start} +#' \item{exon_chromend}{genetic position of exon end} +#' } +"ENSEXONS_37" + + diff --git a/R/toprdata.R b/R/toprdata.R index 5933b07..6b1eb69 100644 --- a/R/toprdata.R +++ b/R/toprdata.R @@ -1,12 +1,14 @@ #' toprdata #' -#' @description Gene and exon datasets to use with the topr package +#' @description Gene and exon datasets to use with the 'topr' package #' @docType package #' @name toprdata #' @section datasets: #' The two datasets are: -#' * \code{\link{ENSGENES}} Gene information -#' * \code{\link{ENSEXONS}} Exon informatino +#' * \code{\link{ENSGENES}} Gene information from genome build GRCh38 +#' * \code{\link{ENSEXONS}} Exon information from genome build GRCh38 +#' * \code{\link{ENSGENES_37}} Gene information from genome build GRCh37 +#' * \code{\link{ENSEXONS_37}} Exon information from genome build GRCh37 #' @examples #' library(toprdata) #' head(ENSGENES) diff --git a/data/ENSEXONS_37.rda b/data/ENSEXONS_37.rda new file mode 100644 index 0000000..3792e6b Binary files /dev/null and b/data/ENSEXONS_37.rda differ diff --git a/data/ENSGENES_37.rda b/data/ENSGENES_37.rda new file mode 100644 index 0000000..d8e5f4a Binary files /dev/null and b/data/ENSGENES_37.rda differ diff --git a/man/ENSEXONS_37.Rd b/man/ENSEXONS_37.Rd new file mode 100644 index 0000000..6590efb --- /dev/null +++ b/man/ENSEXONS_37.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{ENSEXONS_37} +\alias{ENSEXONS_37} +\title{Ensembl exons build HG37 (GRCh37) v40 from gencode} +\format{ +A data frame with 62,739 rows and 7 variables: +\describe{ +\item{chrom}{Chromosome on build version 38 (GRCh38/hg38)} +\item{gene_start}{genetic position of gene start on build version 38} +\item{gene_end}{genetic position of gene end on build version 38 } +\item{gene_symbol}{The name of the gene} +\item{exon_chromstart}{genetic positions of exon start} +\item{exon_chromend}{genetic position of exon end} +} +} +\usage{ +ENSEXONS_37 +} +\description{ +exons on chrY and chrM were excluded from the exon dataset +} +\keyword{datasets} diff --git a/man/ENSGENES_37.Rd b/man/ENSGENES_37.Rd new file mode 100644 index 0000000..57e7cd4 --- /dev/null +++ b/man/ENSGENES_37.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{ENSGENES_37} +\alias{ENSGENES_37} +\title{Ensembl genes build HG37 (GRCh37) v40 from gencode} +\format{ +A data frame with 62,743 rows and 5 variables: +\describe{ +\item{chrom}{Chromosome on build version 38 (GRCh38/hg38)} +\item{gene_start}{genetic position of gene start on build version 38} +\item{gene_end}{genetic position of gene end on build version 38 } +\item{gene_symbol}{The name of the gene} +\item{biotype}{the biotype of the gene} +} +} +\usage{ +ENSGENES_37 +} +\description{ +genes on chrY and chrM were excluded +} +\keyword{datasets} diff --git a/man/toprdata.Rd b/man/toprdata.Rd index 91a707e..3c4a666 100644 --- a/man/toprdata.Rd +++ b/man/toprdata.Rd @@ -5,14 +5,16 @@ \alias{toprdata} \title{toprdata} \description{ -Gene and exon datasets to use with the topr package +Gene and exon datasets to use with the 'topr' package } \section{datasets}{ The two datasets are: \itemize{ -\item \code{\link{ENSGENES}} Gene information -\item \code{\link{ENSEXONS}} Exon informatino +\item \code{\link{ENSGENES}} Gene information from genome build GRCh38 +\item \code{\link{ENSEXONS}} Exon information from genome build GRCh38 +\item \code{\link{ENSGENES_37}} Gene information from genome build GRCh37 +\item \code{\link{ENSEXONS_37}} Exon information from genome build GRCh37 } }