diff --git a/R/HiC2Tree.R b/R/HiC2Tree.R index bf57cfe59f831ae992357e6494ca632c4549d928..8ed773f647e0cbef5a3483e59ad51f2852fdc42d 100644 --- a/R/HiC2Tree.R +++ b/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 diff --git a/man/HiC2Tree.Rd b/man/HiC2Tree.Rd index a4882af53c8999dfc09aac33bd487106995d0f86..1318ae5bd1f156632eec58da467911b559026a77 100644 --- a/man/HiC2Tree.Rd +++ b/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)