diff --git a/DESCRIPTION b/DESCRIPTION index ba7c697..c2dc953 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: HGNChelper Maintainer: Levi Waldron Depends: R (>= 3.5.0), methods, utils Author: Levi Waldron and Markus Riester -Version: 0.8.6 -Date: 2020-9-11 +Version: 0.8.7 +Date: 2020-12-29 License: GPL (>=2.0) Title: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols Description: Contains functions for diff --git a/R/checkGeneSymbols.R b/R/checkGeneSymbols.R index 5599a35..7bfdec2 100755 --- a/R/checkGeneSymbols.R +++ b/R/checkGeneSymbols.R @@ -8,10 +8,10 @@ #' @importFrom methods is #' @importFrom utils read.csv data #' -#' @param x A character vector of gene symbols to check for mogrified or outdated values -#' @param chromosome A integer vector containing the chromosome number you want to -#' specify for each gene provided through the argument \code{x}. It should be the -#' same length as the input for \code{x}. Currently, this argument is applicable +#' @param x A character vector of gene symbols to check for modified or outdated values +#' @param chromosome An optional integer vector containing the chromosome number of each gene +#' provided through the argument \code{x}. It should be the +#' same length as the input for \code{x}. Currently, this argument is implemented #' only for human gene cases. #' @param unmapped.as.na If \code{TRUE} (default), unmapped symbols will appear as #' NA in the \code{Suggested.Symbol} column. If \code{FALSE}, the original unmapped diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..8671c51 --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,13 @@ +.onLoad <- function(libname, pkgname) { + packageStartupMessage( + paste( + "Please cite our software :) \n \n", + "Sehyun Oh et al.", + "HGNChelper: identification and correction of invalid gene symbols for human and mouse.", + "F1000Research 2020, 9:1493.", + "DOI: https://doi.org/10.12688/f1000research.28033.1 \n \n", + "Type `citation('HGNChelper')` for a BibTeX entry." + ) + ) + invisible() +} \ No newline at end of file diff --git a/README.md b/README.md index c679255..8322cec 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,12 @@ # HGNChelper: identification and correction of invalid gene symbols for human and mouse -A [pre-print is available on bioRxiv](https://www.biorxiv.org/content/10.1101/2020.09.16.300632v2). +Please cite our software: + +Oh S, Abdelnabi J, Al-Dulaimi R et al. HGNChelper: identification and +correction of invalid gene symbols for human and mouse. F1000Research 2020, 9:1493 +(https://doi.org/10.12688/f1000research.28033.1) + ## Updating diff --git a/index.md b/index.md index 5494cc1..a27451f 100644 --- a/index.md +++ b/index.md @@ -4,7 +4,12 @@ # HGNChelper: Identification and correction of invalid gene symbols for human and mouse -A [pre-print is available on bioRxiv](https://www.biorxiv.org/content/10.1101/2020.09.16.300632v2). +Please cite our software: + +Oh S, Abdelnabi J, Al-Dulaimi R et al. HGNChelper: identification and +correction of invalid gene symbols for human and mouse. F1000Research +2020, 9:1493 +[https://doi.org/10.12688/f1000research.28033.1](https://doi.org/10.12688/f1000research.28033.1) ## Why HGNChelper? diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..079b076 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,18 @@ +citHeader("Please cite our software :)") + +citEntry(entry = "Article", + title = "HGNChelper: identification and correction of invalid gene symbols for human and mouse", + author = personList(as.person("Sehyun Oh"), as.person("Jasmine Abdelnabi"), + as.person("Ragheed Al-Dulaimi"), as.person("Ayush Aggarwal"), as.person("Marcel Ramos"), + as.person("Carmen Rodriguez Cabrera"), as.person("Tiffany Chan"), + as.person("Sean Davis"), as.person("Markus Riester"), + as.person("Levi Waldron")), + journal = "F1000 Research", + year = "2020", + volume = "9:1493", + textVersion = + paste("Sehyun Oh et al.", + "HGNChelper: identification and correction of invalid gene symbols for human and mouse.", + "F1000Research 2020, 9:1493.", + "DOI: https://doi.org/10.12688/f1000research.28033.1") +) diff --git a/man/checkGeneSymbols.Rd b/man/checkGeneSymbols.Rd index 8dc2a3a..a764ad6 100644 --- a/man/checkGeneSymbols.Rd +++ b/man/checkGeneSymbols.Rd @@ -13,11 +13,11 @@ checkGeneSymbols( ) } \arguments{ -\item{x}{A character vector of gene symbols to check for mogrified or outdated values} +\item{x}{A character vector of gene symbols to check for modified or outdated values} -\item{chromosome}{A integer vector containing the chromosome number you want to -specify for each gene provided through the argument \code{x}. It should be the -same length as the input for \code{x}. Currently, this argument is applicable +\item{chromosome}{An optional integer vector containing the chromosome number of each gene +provided through the argument \code{x}. It should be the +same length as the input for \code{x}. Currently, this argument is implemented only for human gene cases.} \item{unmapped.as.na}{If \code{TRUE} (default), unmapped symbols will appear as