From d53cc84f1113793b551c2f56d1e06411d7ff893a Mon Sep 17 00:00:00 2001
From: Levi Waldron <lwaldron.research@gmail.com>
Date: Fri, 17 May 2024 21:16:35 -0700
Subject: [PATCH] Documentation syntax

---
 R/HGNChelper-package.R    |  3 +++
 R/getCurrentMaps.R        |  2 +-
 man/HGNChelper-package.Rd | 48 ++++++++++++++++++++-------------------
 man/getCurrentMaps.Rd     |  2 +-
 4 files changed, 30 insertions(+), 25 deletions(-)
 create mode 100644 R/HGNChelper-package.R
 mode change 100755 => 100644 man/HGNChelper-package.Rd

diff --git a/R/HGNChelper-package.R b/R/HGNChelper-package.R
new file mode 100644
index 0000000..fd1f8e9
--- /dev/null
+++ b/R/HGNChelper-package.R
@@ -0,0 +1,3 @@
+#' @keywords internal
+"_PACKAGE"
+NULL
\ No newline at end of file
diff --git a/R/getCurrentMaps.R b/R/getCurrentMaps.R
index 2efa5bb..b604b44 100644
--- a/R/getCurrentMaps.R
+++ b/R/getCurrentMaps.R
@@ -6,7 +6,7 @@
 #' then use as an input to the \code{map} argument of \code{checkGeneSymbols}. 
 #' Make sure to change the default \code{species="human"} argument to \code{checkGeneSymbols} 
 #' if you are doing this for mouse. Use \code{getCurrentHumanMap} for HGNC human gene 
-#' symbols from \url{genenames.org} and \code{getCurrentMouseMap} for MGI mouse gene 
+#' symbols from \url{https://www.genenames.org/} and \code{getCurrentMouseMap} for MGI mouse gene 
 #' symbols from \url{https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt}.
 #' @return A \code{data.frame} that can be used for \code{map} argument of \code{checkGeneSymbols} function
 #' @export getCurrentMouseMap getCurrentHumanMap
diff --git a/man/HGNChelper-package.Rd b/man/HGNChelper-package.Rd
old mode 100755
new mode 100644
index ae38975..01af18c
--- a/man/HGNChelper-package.Rd
+++ b/man/HGNChelper-package.Rd
@@ -1,29 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/HGNChelper-package.R
+\docType{package}
 \name{HGNChelper-package}
+\alias{HGNChelper}
 \alias{HGNChelper-package}
-\docType{package}
-\title{Handy functions for working with HGNC gene symbols and
-Affymetrix probeset identifiers.}
-\description{Contains functions for
-identifying and correcting HGNC gene symbols which have been converted
-to date format by Excel, for reversibly converting between HGNC
-symbols and valid R names, identifying invalid HGNC symbols and
-correcting synonyms and outdated symbols which can be mapped to an
-official symbol.}
-\details{
-\tabular{ll}{Package: \tab HGNChelper\cr
-Authors: \tab Levi Waldron and Markus Riester\cr
-Maintainer: \tab Levi Waldron <lwaldron.research@gmail.com>\cr
-Depends: \tab R (>= 3.5.0)\cr
-Version: \tab \Sexpr{packageDescription("HGNChelper")$Version}\cr
-Date: \tab \Sexpr{packageDescription("HGNChelper")$Date}\cr
-License: \tab GPL (>2.0)\cr
-Title: \tab Handy functions for working with HGNC gene symbols and
-Affymetrix probeset identifiers.\cr
-URL: \tab https://waldronlab.io/HGNChelper/\cr
-BugReports: \tab https://github.com/waldronlab/hgnchelper/issues \cr}
+\title{HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols}
+\description{
+Contains functions for identifying and correcting HGNC human gene symbols and MGI mouse gene symbols which have been converted to date format by Excel, withdrawn, or aliased. Also contains functions for reversibly converting between HGNC symbols and valid R names.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/waldronlab/HGNChelper}
+  \item \url{https://waldronlab.io/HGNChelper/}
+  \item Report bugs at \url{https://github.com/waldronlab/HGNChelper/issues}
 }
-\author{Levi Waldron and Markus Riester}
 
-\keyword{ package }
+}
+\author{
+\strong{Maintainer}: Levi Waldron \email{lwaldron.research@gmail.com}
 
+Authors:
+\itemize{
+  \item Sehyun Oh \email{sehyun.oh@sph.cuny.edu}
+  \item Ayush Aggarwal \email{ayush.aggarwal@igib.in}
+  \item Markus Riester \email{Markus.riester@novartis.com}
+}
 
+}
+\keyword{internal}
diff --git a/man/getCurrentMaps.Rd b/man/getCurrentMaps.Rd
index bf7c796..3cf20c1 100644
--- a/man/getCurrentMaps.Rd
+++ b/man/getCurrentMaps.Rd
@@ -18,7 +18,7 @@ these functions to get the most current lists of valid symbols, which you can
 then use as an input to the \code{map} argument of \code{checkGeneSymbols}. 
 Make sure to change the default \code{species="human"} argument to \code{checkGeneSymbols} 
 if you are doing this for mouse. Use \code{getCurrentHumanMap} for HGNC human gene 
-symbols from \url{genenames.org} and \code{getCurrentMouseMap} for MGI mouse gene 
+symbols from \url{https://www.genenames.org/} and \code{getCurrentMouseMap} for MGI mouse gene 
 symbols from \url{https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt}.
 }
 \examples{