From 93d2fb110c19e78f530efd8adb8956b0263205e5 Mon Sep 17 00:00:00 2001
From: Charles Plessy <charles-plessy@.oist.jp>
Date: Fri, 10 May 2024 08:32:52 +0900
Subject: [PATCH] Use Roxygen to transfer package DESCRIPTION to documentation.

Also take this opportunity to revamp package description.
---
 DESCRIPTION          | 16 +++++++++++++---
 R/CAGEr.R            | 20 --------------------
 man/CAGEr-package.Rd | 31 +++++++++++++++++--------------
 3 files changed, 30 insertions(+), 37 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 26d8f45..e99b4a4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -48,9 +48,18 @@ Suggests:
     BiocStyle,
     knitr,
     rmarkdown
-Description: Preprocessing of CAGE sequencing data, identification and
- normalization of transcription start sites and downstream analysis of
- transcription start sites clusters (promoters).
+Description: The _CAGEr_ package identifies transcription start sites (TSS) and
+ their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data.
+ It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and
+ aggregates them across multiple CAGE experiments to construct consensus
+ clusters (CC) representing the promoterome.  CAGEr provides functions to
+ profile expression levels of these clusters by cumulative expression and
+ rarefaction analysis, and outputs the plots in ggplot2 format for further
+ facetting and customisation.  After clustering, CAGEr performs analyses of
+ promoter width and detects differential usage of TSSs (promoter shifting)
+ between samples.  CAGEr also exports its data as genome browser tracks, and as
+ R objects for downsteam expression analysis by other Bioconductor packages
+ such as DESeq2, CAGEfightR, or seqArchR.
 License: GPL-3
 biocViews: Preprocessing, Sequencing, Normalization, FunctionalGenomics, Transcription, GeneExpression, Clustering, Visualization
 Collate: 
@@ -63,6 +72,7 @@ Collate:
     'Annotations.R'
     'AggregationMethods.R'
     'CAGEfightR.R'
+    'CAGEr-package.R'
     'CorrelationMethods.R'
     'CumulativeDistributionFunctions.R'
     'GetMethods.R'
diff --git a/R/CAGEr.R b/R/CAGEr.R
index 8ed72b7..380f5b8 100644
--- a/R/CAGEr.R
+++ b/R/CAGEr.R
@@ -1,25 +1,5 @@
 #' @include CAGEexp.R CTSS.R
 NULL
-
-#' Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for
-#' precise mapping of transcription start sites and promoterome mining
-#' 
-#' The _CAGEr_ package performs identification of transcription start sites and
-#' frequency of their usage from input CAGE sequencing data, normalization of
-#' raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their
-#' aggregation across multiple CAGE experiments to construct the promoterome.
-#' It manipulates multiple CAGE experiments at once, performs expression
-#' profiling across experiments both at level of individual TSSs and clusters of
-#' TSSs, exports several different types of track files for visualization in the
-#' UCSC Genome Browser, performs analysis of promoter width and detects
-#' differential usage of TSSs (promoter shifting) between samples.  Multicore
-#' option for parallel processing is supported on Unix-like platforms.
-#' 
-#' @author Vanja Haberle
-#' 
-#' @docType package
-#' @name CAGEr-package
-NULL
  
 #' CAGEr objects
 #' 
diff --git a/man/CAGEr-package.Rd b/man/CAGEr-package.Rd
index e633f43..b4eb60f 100644
--- a/man/CAGEr-package.Rd
+++ b/man/CAGEr-package.Rd
@@ -1,22 +1,25 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CAGEr.R
+% Please edit documentation in R/CAGEr-package.R
 \docType{package}
 \name{CAGEr-package}
 \alias{CAGEr-package}
-\title{Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for
-precise mapping of transcription start sites and promoterome mining}
+\title{CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining}
 \description{
-The \emph{CAGEr} package performs identification of transcription start sites and
-frequency of their usage from input CAGE sequencing data, normalization of
-raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their
-aggregation across multiple CAGE experiments to construct the promoterome.
-It manipulates multiple CAGE experiments at once, performs expression
-profiling across experiments both at level of individual TSSs and clusters of
-TSSs, exports several different types of track files for visualization in the
-UCSC Genome Browser, performs analysis of promoter width and detects
-differential usage of TSSs (promoter shifting) between samples.  Multicore
-option for parallel processing is supported on Unix-like platforms.
+The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
 }
 \author{
-Vanja Haberle
+\strong{Maintainer}: Charles Plessy \email{charles.plessy@oist.jp}
+
+Authors:
+\itemize{
+  \item Vanja Haberle \email{vanja.haberle@gmail.com}
 }
+
+Other contributors:
+\itemize{
+  \item Damir Baranasic \email{damir.baranasic@lms.mrc.ac.uk} [contributor]
+  \item Sarvesh Nikumbh \email{s.nikumbh@lms.mrc.ac.uk} [contributor]
+}
+
+}
+\keyword{internal}