correcting a minor problem in documentation + improved a bit wording

R/HiC2Tree.R

@@ -2,7 +2,7 @@
 #'
 #' @description This function converts Hi-C data into trees, using the adjclust
 #' algorithm. It takes as input a file path vector, the format of the input
-#' data, the bins size of the Hi-C array, the chromosomes to be included in the
+#' data, the bin size of the Hi-C array, the chromosomes to be included in the
 #' analysis, and the number of replicates. It returns a list containing all
 #' trees, metadata, index and treediff results.
 #'
@@ -10,13 +10,14 @@
 #' @param format A character vector indicating the format of the input data:
 #' "tabular", "cooler", "juicer", or "HiC-Pro".
 #' @param binsize An integer indicating the bin size of the Hi-C matrix.
-#' @param index Index of the input data, only needed with the "HiC-Pro" format.
+#' @param index A character indicating the path of the index for the input data.
+#' Required (and used) only with the "HiC-Pro" format.
 #' @param chromosomes A vector containing the chromosomes to be included in the
 #' analysis.
 #' @param replicates An integer indicating the number of replicates to be used
 #' in treediff.
-#'
-#' @return A list containing:
+#' 
+#' @return A list containing: 
 #' \itemize{
 #'   \item{trees}{ A list of all trees.}
 #'   \item{metadata}{ A data frame containing the following columns: names (name
@@ -48,7 +49,7 @@
 #' format <- rep(rep("HiC-Pro", 6), nb_chr)
 #' binsize <- 200000
 #' files <- system.file("extdata", unlist(all_mat_chr), package = "treediff")
-#' replicates <- c(3,3)
+#' replicates <- c(3, 3)
 #'
 #' HiC2Tree(files, format, binsize, index, chromosomes, replicates)
 #'
@@ -376,7 +377,6 @@ normalizeCount.HiCDOCDataSetList <- function(count_matrice){
 #' @param mat A matrix containing the data to cluster. It should have columns
 #' named 'index1', 'index2', 'chromosome and one column for each matrices.
 #'
-#' @return
 #' @return A list containing the following objects:
 #' \describe{
 #'   \item{trees}{ A list of hierarchical clustering trees, one for each cluster

man/HiC2Tree.Rd

@@ -14,7 +14,8 @@ HiC2Tree(files, format, binsize = NULL, index = NULL, chromosomes, replicates)
 
 \item{binsize}{An integer indicating the bin size of the Hi-C matrix.}
 
-\item{index}{Index of the input data, only needed with the "HiC-Pro" format.}
+\item{index}{A character indicating the path of the index for the input data.
+Required (and used) only with the "HiC-Pro" format.}
 
 \item{chromosomes}{A vector containing the chromosomes to be included in the
 analysis.}
@@ -23,7 +24,7 @@ analysis.}
 in treediff.}
 }
 \value{
-A list containing:
+A list containing: 
 \itemize{
   \item{trees}{ A list of all trees.}
   \item{metadata}{ A data frame containing the following columns: names (name
@@ -36,7 +37,7 @@ A list containing:
 \description{
 This function converts Hi-C data into trees, using the adjclust
 algorithm. It takes as input a file path vector, the format of the input
-data, the bins size of the Hi-C array, the chromosomes to be included in the
+data, the bin size of the Hi-C array, the chromosomes to be included in the
 analysis, and the number of replicates. It returns a list containing all
 trees, metadata, index and treediff results.
 }
@@ -61,7 +62,7 @@ package = "treediff")
 format <- rep(rep("HiC-Pro", 6), nb_chr)
 binsize <- 200000
 files <- system.file("extdata", unlist(all_mat_chr), package = "treediff")
-replicates <- c(3,3)
+replicates <- c(3, 3)
 
 HiC2Tree(files, format, binsize, index, chromosomes, replicates)