diff --git a/DESCRIPTION b/DESCRIPTION index ff3ca06..dc28947 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,6 @@ Description: The pattern of digestion and protection from DNA nucleases such over single or aggregated genomic loci of interest. URL: https://github.com/js2264/VplotR BugReports: https://github.com/js2264/VplotR/issues -RoxygenNote: 7.1.1 Depends: R (>= 4.0), GenomicRanges, @@ -55,3 +54,4 @@ biocViews: ATACSeq, Alignment License: GPL (>= 3) +RoxygenNote: 7.2.3 diff --git a/NAMESPACE b/NAMESPACE index 7a14c86..a6def14 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -30,11 +30,11 @@ import(RColorBrewer) import(Rsamtools) import(S4Vectors) import(ggplot2) -import(magrittr) import(parallel) import(reshape2) importFrom(cowplot,plot_grid) importFrom(graphics,hist) +importFrom(magrittr,`%>%`) importFrom(methods,as) importFrom(methods,is) importFrom(stats,qt) diff --git a/R/fragsize.R b/R/fragsize.R index 2582ed7..90ca38f 100644 --- a/R/fragsize.R +++ b/R/fragsize.R @@ -15,10 +15,10 @@ #' fragment size distribution #' @return A list of tbl, one for each .bam file. #' -#' @import magrittr #' @import parallel #' @import IRanges #' @import GenomicRanges +#' @importFrom magrittr `%>%` #' @importFrom zoo rollmean #' @importFrom methods is #' @importFrom graphics hist diff --git a/R/vmat_utils.R b/R/vmat_utils.R index 9301d62..ffa10b2 100644 --- a/R/vmat_utils.R +++ b/R/vmat_utils.R @@ -12,7 +12,6 @@ #' @param ylims The y limits of the computed Vmat #' @return A table object #' -#' @import magrittr #' @import S4Vectors #' @import GenomicRanges #' @import IRanges diff --git a/man/importPEBamFiles.Rd b/man/importPEBamFiles.Rd index 1438c01..90eb844 100644 --- a/man/importPEBamFiles.Rd +++ b/man/importPEBamFiles.Rd @@ -18,8 +18,8 @@ importPEBamFiles( \item{files}{character vector, each element of the vector is the path of an individual .bam file.} -\item{genome}{character, genome ID (e.g. sacCer3, ce11, dm6, danRer10, -mm10 or hg38).} +\item{genome}{character, genome ID (e.g. "sacCer3", "ce11", "dm6", +"mm10" or "hg38").} \item{where}{GRanges, only import the fragments mapping to the input GRanges (can fasten the import process a lot).} diff --git a/vignettes/VplotR.Rmd b/vignettes/VplotR.Rmd index bea47c0..38a39c7 100644 --- a/vignettes/VplotR.Rmd +++ b/vignettes/VplotR.Rmd @@ -17,7 +17,6 @@ knitr::opts_chunk$set( suppressPackageStartupMessages({ library(GenomicRanges) library(ggplot2) - library(magrittr) library(VplotR) }) ```