Added extdata.R plus documentation; updated NEWS

NEWS

@@ -1,6 +1,14 @@
 # All changes to RNAModR are documented here
 
 
+## Version 0.2.3
+
+- In `plot.R`: Added `plotOverlap`
+- In `helper.R`: `LoadRefTx` now performs version checks on the major, minor
+  and patch version level
+- Added `extdata.R` with details on and references to all internal raw datasets
+
+
 ## Version 0.2.2
 
 - In `plot.R`: Added `PlotRelStartStopEnrichment`

R/extdata.R

@@ -0,0 +1,53 @@
+#' Internal raw datasets.
+#'
+#' Internal raw datasets in BED6 format. All genome positions where converted 
+#' to the most recent genome assembly version; i.e. for human data, all
+#' positions are given in GRCh38/hg38 coordinates. For mouse data, positions
+#' are given in mm10 coordinates.
+#' 
+#' \describe{
+#'     \item{\code{bsRNAseq_m5C_Squires2012_hg38.bed}}{
+#'     bsRNA-seq 5-methylcytosine (m5C) sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/22344696}}
+#'     \item{\code{HITSCLIP_eIF4A3_Sauliere2012_hg38.bed}}{
+#'     HITSCLIP eIF4AIII binding sites. 
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/23085716}}
+#'     \item{\code{MeRIPseq_m1A_Dominissini2016_hg38.bed}}{
+#'     MeRIP-seq N(1)-methyladenosine (m1A) sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/26863196}}
+#'     \item{\code{miCLIP_m6A_Linder2015_hg38.bed}}{
+#'     miCLIP N(6)-methyladenosine (m6A) sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/26121403}}
+#'     \item{\code{PARCLIP_AGO1234_Hafner2010_hg38.bed}}{
+#'     PAR-CLIP AGO1-4 binding sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/20371350}}
+#'     \item{\code{PARCLIP_eIF3_Meyer2015_hg38.bed}}{
+#'     PAR-CLIP eIF3 binding sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/26593424}}
+#'     \item{\code{PARCLIP_eIF3_Lee2015_hg38.bed}}{
+#'     PAR-CLIP eIF3 binding sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/25849773}}
+#'     \item{\code{PARCLIP_YTHDF2_Wang2014_hg38.bed}}{
+#'     PAR-CLIP YTHDF2 binding sites.
+#'     Reference: \url{https://www.ncbi.nlm.nih.gov/pubmed/24284625}}
+#'     \item{\code{PseudoU_Schwartz2014_Li2015_hg38.bed}}{
+#'     Merged Psi-seq and CeU-seq pseudouridine (Psi) sites.
+#'     References: \url{https://www.ncbi.nlm.nih.gov/pubmed/25219674},
+#'     \url{https://www.ncbi.nlm.nih.gov/pubmed/26075521}}
+#'     \item{\code{TargetScan_miRNAtargets_hg38.bed}}{
+#'     TargetScan-based miRNA target sites.
+#'     Reference: \url{http://www.targetscan.org/vert_72/}}
+#' }
+#'
+#' @name Datasets
+#' @rdname Datasets
+#'
+#' @author Maurits Evers, \email{maurits.evers@@anu.edu.au}
+#' @examples
+#' \dontrun{
+#' bedFile <- ReadBED(system.file(
+#'     "extdata",
+#'     "miCLIP_m6A_Linder2015_hg38.bed",
+#'     package = "RNAModR")
+#' }
+NULL