Update documentation to reflect support for mouse genome

NEWS.md

@@ -1,9 +1,14 @@
-## CHANGES IN VERSION 1.10.1
+## CHANGES IN VERSION 1.10.1 [HOTFIX]
 
 ### Bug Fixes
 
 * `prepare_output_build`
   - Fix support for mouse genome builds (mm9 and mm10).
+
+### Documentation
+
+* `Epicompare.Rmd`
+  - Mention support for mouse genome builds.
 
 ## CHANGES IN VERSION 1.9.5
 

R/EpiCompare.R

@@ -11,7 +11,7 @@
 #' and paths.Files must be listed and named using \code{list()}.
 #' E.g. \code{list("name1"=file1, "name2"=file2)}. If no names are specified,
 #' default file names will be assigned.
-#' @param genome_build A named list indicating the human genome build used to
+#' @param genome_build A named list indicating the genome build used to
 #' generate each of the following inputs:
 #' \itemize{
 #' \item{"peakfiles" : }{Genome build for the \code{peakfiles} input.
@@ -27,10 +27,12 @@
 #' This should \emph{only} be done in situations where all three inputs
 #' (\code{peakfiles}, \code{reference}, \code{blacklist}) are of the same
 #' genome build. For example:\cr
-#' \code{genome_build = "hg19"}
+#' \code{genome_build = "hg19"}\cr\cr
+#' Supported genome builds are: "hg19", "hg38", "mm9" and "mm10".
 #' @param genome_build_output Genome build to standardise all inputs to.
 #' Liftovers will be performed automatically as needed.
-#' Default: "hg19".
+#' Default: "hg19".\cr\cr
+#' \strong{Note:} Cross-species liftovers are supported.
 #' @param blacklist A \link[GenomicRanges]{GRanges} object
 #'  containing blacklisted genomic regions.
 #' Blacklists included in \pkg{EpiCompare} are:

inst/markdown/EpiCompare.Rmd

@@ -82,7 +82,7 @@ if(params$save_output){
 # or... genome_build <- "hg19"
 builds <- prepare_genome_builds(genome_build = params$genome_build,
                                 blacklist = params$blacklist)
-## Standardise all data to hg19 build 
+## Standardise all data to specified build 
 output_build <- prepare_output_build(params$genome_build_output)
 
 #### ------ Prepare peaklist(s) ------ ####

vignettes/EpiCompare.Rmd

@@ -46,8 +46,8 @@ experimental conditions and data analysis workflows of one technology. This
 can help researchers to establish a consensus regarding the optimal use of the 
 method. 
 
-Currently, *EpiCompare* only works for human genome as it uses human-based 
-hg19 and/or hg38 genome references. 
+Currently, *EpiCompare* supports human and mouse genomes (hg19, hg38, mm9 and
+mm10).
 
 # Data