fix: rm magrittr general import to avoid conflict with GenomicRanges:…

…:substract

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

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)

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

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

vignettes/VplotR.Rmd

@@ -17,7 +17,6 @@ knitr::opts_chunk$set(
 suppressPackageStartupMessages({
     library(GenomicRanges)
     library(ggplot2)
-    library(magrittr)
     library(VplotR)
 })
 ```