From 00f215b16b1c03d9a79108493293935796b3d606 Mon Sep 17 00:00:00 2001
From: borauyar <bora.uyar@mdc-berlin.de>
Date: Wed, 6 Sep 2017 10:26:08 +0200
Subject: [PATCH] changed quiet argument to debug in importBed function and
 updated relevant documentation, examples, and functions

---
 R/meta_analysis_functions.R |  6 +++---
 R/report_functions.R        | 10 +++++-----
 man/importBed.Rd            |  4 ++--
 man/importBedFiles.Rd       |  4 ++--
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/meta_analysis_functions.R b/R/meta_analysis_functions.R
index 1d4798d..771f7f7 100644
--- a/R/meta_analysis_functions.R
+++ b/R/meta_analysis_functions.R
@@ -17,15 +17,15 @@
 #' # when importing multiple bed files with different column names, it 
 #' # is required to pass the common column names to be parsed from the 
 #' # bed files
-#' bedData <- importBedFiles(filePaths = c(input1, input2), quiet = TRUE,
-#'                 colnames = c('chrom', 'start', 'end', 'strand'))
+#' bedData <- importBedFiles(filePaths = c(input1, input2),
+#'                  colnames = c('chrom', 'start', 'end', 'strand'))
 #' 
 #' @importFrom GenomicRanges GRangesList
 #' @importFrom pbapply pbsapply
 #' @export
 importBedFiles <- function(filePaths, ...) {
   bedData <- GenomicRanges::GRangesList(pbapply::pbsapply(filePaths, function(f) {
-    RCAS::importBed(filePath = f, quiet = TRUE, ...)
+    RCAS::importBed(filePath = f, debug = FALSE, ...)
   }, USE.NAMES = TRUE))
   names(bedData) <- gsub(pattern = '.bed$', 
                          replacement = '', 
diff --git a/R/report_functions.R b/R/report_functions.R
index e863288..57e3fd9 100644
--- a/R/report_functions.R
+++ b/R/report_functions.R
@@ -96,7 +96,7 @@ importGtf <- function (filePath,  saveObjectAsRds = TRUE, readFromRds = TRUE,
 #'   convert the \code{seqlevelsStyle} to 'UCSC' and apply
 #'   \code{keepStandardChromosomes} function to only keep data from the standard
 #'   chromosomes
-#' @param quiet TRUE/FALSE (default:FALSE). Set to TRUE to turn off messages
+#' @param debug TRUE/FALSE (default:TRUE). Set to FALSE to turn off messages
 #' @param ... Other arguments passed to rtracklayer::import.bed function
 #' @return A \code{GRanges} object containing the coordinates of the intervals
 #'   from an input BED file
@@ -109,23 +109,23 @@ importGtf <- function (filePath,  saveObjectAsRds = TRUE, readFromRds = TRUE,
 #' @importFrom GenomeInfoDb seqlevelsStyle
 #' @importFrom GenomeInfoDb keepStandardChromosomes
 #' @export
-importBed <- function (filePath, sampleN = 0, keepStandardChr = TRUE, quiet = FALSE, ...) {
+importBed <- function (filePath, sampleN = 0, keepStandardChr = TRUE, debug = TRUE, ...) {
 
   if (file.exists(filePath)) {
     data = rtracklayer::import.bed(filePath, ...)
-    if(quiet == FALSE) {
+    if(debug == TRUE) {
       cat('Processing',filePath,'\n')
     }
     if (keepStandardChr == TRUE) {
       GenomeInfoDb::seqlevelsStyle(data) <- 'UCSC'
-      if(quiet == FALSE) {
+      if(debug == TRUE) {
         cat('Keeping standard chromosomes only\n')
       }
       data <- GenomeInfoDb::keepStandardChromosomes(data, pruning.mode = 'coarse')
     }
 
     if (sampleN > 0 && sampleN < length(data)) {
-      if(quiet == FALSE) {
+      if(debug == TRUE) {
         cat ('Downsampling intervals to size:',sampleN,'\n')
       }
       data <- data[sample(x = 1:length(data), size = sampleN)]
diff --git a/man/importBed.Rd b/man/importBed.Rd
index 50af924..2c555e6 100644
--- a/man/importBed.Rd
+++ b/man/importBed.Rd
@@ -4,7 +4,7 @@
 \alias{importBed}
 \title{importBed}
 \usage{
-importBed(filePath, sampleN = 0, keepStandardChr = TRUE, quiet = FALSE,
+importBed(filePath, sampleN = 0, keepStandardChr = TRUE, debug = TRUE,
   ...)
 }
 \arguments{
@@ -20,7 +20,7 @@ convert the \code{seqlevelsStyle} to 'UCSC' and apply
 \code{keepStandardChromosomes} function to only keep data from the standard
 chromosomes}
 
-\item{quiet}{TRUE/FALSE (default:FALSE). Set to TRUE to turn off messages}
+\item{debug}{TRUE/FALSE (default:TRUE). Set to FALSE to turn off messages}
 
 \item{...}{Other arguments passed to rtracklayer::import.bed function}
 }
diff --git a/man/importBedFiles.Rd b/man/importBedFiles.Rd
index a56e512..78979f0 100644
--- a/man/importBedFiles.Rd
+++ b/man/importBedFiles.Rd
@@ -28,7 +28,7 @@ keepStandardChr = TRUE)
 # when importing multiple bed files with different column names, it 
 # is required to pass the common column names to be parsed from the 
 # bed files
-bedData <- importBedFiles(filePaths = c(input1, input2), quiet = TRUE,
-                colnames = c('chrom', 'start', 'end', 'strand'))
+bedData <- importBedFiles(filePaths = c(input1, input2),
+                 colnames = c('chrom', 'start', 'end', 'strand'))
 
 }