Use Roxygen to transfer package DESCRIPTION to documentation.

Also take this opportunity to revamp package description.

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'

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
 #'