Adding encoding UTF-8 to man pages

DESCRIPTION

@@ -12,7 +12,7 @@ Description: This package compares genomic positions and genomic ranges from
     peaks and nucleosome positions, the replication of an experiment may result 
     in slight differences between predicted values. This package enables the 
     conciliation of the results into consensus regions.
-Authors@R: c(person("Astrid", "Deschenes", email="[email protected]", 
+Authors@R: c(person("Astrid", "Deschênes", email="[email protected]", 
     role=c("cre","aut"), comment=c(ORCID="0000-0001-7846-6749")), 
     person("Fabien Claude", "Lamaze", email="[email protected]", 
     role=c("ctb")),
@@ -39,10 +39,11 @@ Suggests:
     rmarkdown,
     RUnit
 License: Artistic-2.0
+Encoding: UTF-8
 URL: https://github.com/adeschen/consensusSeekeR
 BugReports: https://github.com/adeschen/consensusSeekeR/issues
 VignetteBuilder: knitr
 NeedsCompilation: no
 biocViews: BiologicalQuestion, ChIPSeq, Genetics, MultipleComparison,
     Transcription, PeakDetection, Sequencing, Coverage
-RoxygenNote: 7.0.2
+RoxygenNote: 7.2.3

R/consensusSeekeR.R

@@ -18,7 +18,7 @@
 #' Arnaud Droit
 #'
 #' Maintainer:
-#' Astrid Deschenes <adeschen@@hotmail.com>
+#' Astrid Deschênes <[email protected]>
 #'
 #' @seealso
 #' \itemize{
@@ -28,6 +28,7 @@
 #' sharing the same features in more than one experiment. }
 #' }
 #'
+#' @encoding UTF-8
 #' @keywords package
 NULL
 

R/findConsensusPeakRegions.R

@@ -82,7 +82,6 @@
 #' consensus regions.
 #' }
 #'
-#' @author Astrid Deschenes
 #' @import BiocGenerics IRanges GenomeInfoDb GenomicRanges
 #' @importFrom stringr str_split
 #' @importFrom BiocParallel bplapply SnowParam SerialParam
@@ -128,6 +127,8 @@
 #' head(results$consensusRanges, 2)
 #'
 #' @importFrom GenomicRanges split
+#' @author Astrid Deschênes
+#' @encoding UTF-8
 #' @export
 findConsensusPeakRegions <- function(narrowPeaks, peaks, chrInfo,
                                 extendingSize = 250,

R/findConsensusPeakRegionsIntern.R

@@ -74,9 +74,10 @@
 #'     minNbrExp = 2,
 #'     nbrThreads = 1)
 #'
-#' @author Astrid Deschenes
+#' @author Astrid Deschênes
 #' @import GenomeInfoDb
 #' @importFrom methods is
+#' @encoding UTF-8
 #' @keywords internal
 findConsensusPeakRegionsValidation <- function(narrowPeaks, peaks, chrList,
             extendingSize, expandToFitPeakRegion, shrinkToFitPeakRegion,
@@ -157,10 +158,10 @@ findConsensusPeakRegionsValidation <- function(narrowPeaks, peaks, chrList,
     }
 
     if (minNbrExp > length(unique(names(peaks)))) {
-        stop(paste0("minNbrExp must be inferior or equal to the number ",
+        stop("minNbrExp must be inferior or equal to the number ",
                     "of experiments presents in peaks. The number of",
                     "experiments is known by the number of differents ",
-                    "row names in peaks."))
+                    "row names in peaks.")
     }
 
     if (!isInteger(nbrThreads) || nbrThreads < 1 ) {
@@ -183,7 +184,8 @@ findConsensusPeakRegionsValidation <- function(narrowPeaks, peaks, chrList,
 #'
 #' @return \code{TRUE} is the parameter is a integer; otherwise \code{FALSE}
 #'
-#' @author Astrid Deschenes
+#' @author Astrid Deschênes
+#' @encoding UTF-8
 #' @keywords internal
 isInteger <- function(value) {
     result <- length(value) == 1
@@ -244,9 +246,10 @@ isInteger <- function(value) {
 #'
 #' @return an object of \code{class} "commonFeatures".
 #'
-#' @author Astrid Deschenes
+#' @author Astrid Deschênes
 #' @import BiocGenerics IRanges GenomeInfoDb GenomicRanges
 #' @importFrom stringr str_split
+#' @encoding UTF-8
 #' @keywords internal
 findConsensusPeakRegionsForOneChrom <- function(chrName, allPeaks,
                                                 allNarrowPeaks, extendingSize,
@@ -448,8 +451,9 @@ findConsensusPeakRegionsForOneChrom <- function(chrName, allPeaks,
 #'
 #' @return an object of \code{class} "commonFeatures".
 #'
-#' @author Astrid Deschenes
+#' @author Astrid Deschênes
 #' @import BiocGenerics IRanges GenomicRanges
+#' @encoding UTF-8
 #' @keywords internal
 refineRegion <- function(peaks, setPeaks, extendingSize,
                                 region_width, currentPeak) {