diff --git a/DESCRIPTION b/DESCRIPTION index d18c7d9..c36b76c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.9.10 +Version: 1.10.1 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", diff --git a/NEWS.md b/NEWS.md index 9607ab7..0c38d86 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,15 @@ +## 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 ### New features diff --git a/R/EpiCompare.R b/R/EpiCompare.R index 4989726..2a99c55 100644 --- a/R/EpiCompare.R +++ b/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: diff --git a/R/prepare_output_build.R b/R/prepare_output_build.R index 3bb1c2f..404b171 100644 --- a/R/prepare_output_build.R +++ b/R/prepare_output_build.R @@ -1,9 +1,10 @@ prepare_output_build <- function(genome_build_output){ - opts <- c("hg19","hg38") + opts <- c("hg19","hg38","mm9","mm10") if(is.null(genome_build_output) || missing(genome_build_output) || (!tolower(genome_build_output) %in% opts)){ - stop("Must provide valid genome_build_output: 'hg19' or 'hg38'") + stop("Must provide valid genome_build_output: ", + "'hg19', 'hg38', 'mm9', or 'mm10'") } return(tolower(genome_build_output)[[1]]) } diff --git a/README.md b/README.md index e6b79f0..318ba7c 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,15 @@ ⚖EpiCompare⚖
QC and Benchmarking of Epigenomic Datasets ================
-[![](https://img.shields.io/badge/release%20version-1.9.3-green.svg)](https://www.bioconductor.org/packages/EpiCompare) -[![](https://img.shields.io/badge/download-27/month-green.svg)](https://bioconductor.org/packages/stats/bioc/EpiCompare) -[![](https://img.shields.io/badge/download-1266/total-green.svg)](https://bioconductor.org/packages/stats/bioc/EpiCompare) +[![](https://img.shields.io/badge/release%20version-1.10.0-green.svg)](https://www.bioconductor.org/packages/EpiCompare) +[![](https://img.shields.io/badge/download-47/month-green.svg)](https://bioconductor.org/packages/stats/bioc/EpiCompare) +[![](https://img.shields.io/badge/download-1451/total-green.svg)](https://bioconductor.org/packages/stats/bioc/EpiCompare) [![download](http://www.bioconductor.org/shields/downloads/release/EpiCompare.svg)](https://bioconductor.org/packages/stats/bioc/EpiCompare) [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) [![](https://img.shields.io/badge/doi-https://doi.org/10.1101/2022.07.22.501149-blue.svg)](https://doi.org/https://doi.org/10.1101/2022.07.22.501149)
-[![](https://img.shields.io/badge/devel%20version-1.9.10-black.svg)](https://github.com/neurogenomics/EpiCompare) +[![](https://img.shields.io/badge/devel%20version-1.10.1-black.svg)](https://github.com/neurogenomics/EpiCompare) [![](https://img.shields.io/github/languages/code-size/neurogenomics/EpiCompare.svg)](https://github.com/neurogenomics/EpiCompare) [![](https://img.shields.io/github/last-commit/neurogenomics/EpiCompare.svg)](https://github.com/neurogenomics/EpiCompare/commits/master)
[![R build @@ -22,7 +22,7 @@ Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts, Hiranyamaya Dash
-Updated: Oct-18-2024 +Updated: Jan-15-2025
# Introduction @@ -384,9 +384,9 @@ Imperial College London utils::sessionInfo() ``` - ## R version 4.4.1 (2024-06-14) + ## R version 4.4.2 (2024-10-31) ## Platform: aarch64-apple-darwin20 - ## Running under: macOS 15.0.1 + ## Running under: macOS Sequoia 15.2 ## ## Matrix products: default ## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib @@ -402,22 +402,21 @@ utils::sessionInfo() ## [1] stats graphics grDevices utils datasets methods base ## ## loaded via a namespace (and not attached): - ## [1] gtable_0.3.5 jsonlite_1.8.9 renv_1.0.11 - ## [4] dplyr_1.1.4 compiler_4.4.1 BiocManager_1.30.25 + ## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11 + ## [4] dplyr_1.1.4 compiler_4.4.2 BiocManager_1.30.25 ## [7] tidyselect_1.2.1 rvcheck_0.2.1 scales_1.3.0 ## [10] yaml_2.3.10 fastmap_1.2.0 here_1.0.1 ## [13] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3 - ## [16] knitr_1.48 yulab.utils_0.1.7 tibble_3.2.1 - ## [19] desc_1.4.3 dlstats_0.1.7 rprojroot_2.0.4 - ## [22] munsell_0.5.1 pillar_1.9.0 RColorBrewer_1.1-3 - ## [25] rlang_1.1.4 utf8_1.2.4 badger_0.2.4 - ## [28] xfun_0.48 fs_1.6.4 cli_3.6.3 - ## [31] magrittr_2.0.3 rworkflows_1.0.2 digest_0.6.37 - ## [34] grid_4.4.1 rstudioapi_0.16.0 lifecycle_1.0.4 - ## [37] vctrs_0.6.5 evaluate_1.0.1 glue_1.8.0 - ## [40] data.table_1.16.2 fansi_1.0.6 colorspace_2.1-1 - ## [43] rmarkdown_2.28 tools_4.4.1 pkgconfig_2.0.3 - ## [46] htmltools_0.5.8.1 + ## [16] knitr_1.49 yulab.utils_0.1.9 tibble_3.2.1 + ## [19] desc_1.4.3 dlstats_0.1.7 munsell_0.5.1 + ## [22] rprojroot_2.0.4 pillar_1.10.1 RColorBrewer_1.1-3 + ## [25] rlang_1.1.4 badger_0.2.4 xfun_0.50 + ## [28] fs_1.6.5 cli_3.6.3 magrittr_2.0.3 + ## [31] rworkflows_1.0.3 digest_0.6.37 grid_4.4.2 + ## [34] rstudioapi_0.17.1 lifecycle_1.0.4 vctrs_0.6.5 + ## [37] evaluate_1.0.1 glue_1.8.0 data.table_1.16.4 + ## [40] colorspace_2.1-1 rmarkdown_2.29 tools_4.4.2 + ## [43] pkgconfig_2.0.3 htmltools_0.5.8.1 diff --git a/inst/markdown/EpiCompare.Rmd b/inst/markdown/EpiCompare.Rmd index 476c42e..ac025e8 100644 --- a/inst/markdown/EpiCompare.Rmd +++ b/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) ------ #### diff --git a/man/EpiCompare.Rd b/man/EpiCompare.Rd index 3e84d19..a45e2df 100644 --- a/man/EpiCompare.Rd +++ b/man/EpiCompare.Rd @@ -45,7 +45,7 @@ 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.} -\item{genome_build}{A named list indicating the human genome build used to +\item{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. @@ -61,11 +61,13 @@ Alternatively, you can supply a single character string instead of a list. 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".} \item{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.} \item{blacklist}{A \link[GenomicRanges]{GRanges} object containing blacklisted genomic regions. diff --git a/man/prepare_genome_builds.Rd b/man/prepare_genome_builds.Rd index 656a8c1..b3d0d4a 100644 --- a/man/prepare_genome_builds.Rd +++ b/man/prepare_genome_builds.Rd @@ -7,7 +7,7 @@ prepare_genome_builds(genome_build, blacklist = NULL) } \arguments{ -\item{genome_build}{A named list indicating the human genome build used to +\item{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. @@ -23,7 +23,8 @@ Alternatively, you can supply a single character string instead of a list. 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".} \item{blacklist}{A \link[GenomicRanges]{GRanges} object containing blacklisted genomic regions. diff --git a/vignettes/EpiCompare.Rmd b/vignettes/EpiCompare.Rmd index 6902342..07730a9 100644 --- a/vignettes/EpiCompare.Rmd +++ b/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