add citation to F1000 Research

DESCRIPTION

@@ -2,8 +2,8 @@ Package: HGNChelper
 Maintainer: Levi Waldron <[email protected]>
 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

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-#' @param x A character vector of gene symbols to check for mogrified or outdated values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+#' @param x A character vector of gene symbols to check for modified or outdated values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 

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()
+}

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
 

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?
 

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")
+)