#' build GenomicInteraction from matrix files
#'
#' The hicpro software generates a sparse matrix format that
#' includes three columns:
#'
#' bin_i
#' bin_j
#' count_ij
#'
#' A BED file (either _abs or _ord bed file is fine) is also generated
#' that includes a fourth column, the bin number. A join on
#' the bin numbers and the bed file is necessary to produce a
#' GenomicInteractions object.
#'
#' @param matrixfile
#' @param bedfile
#'
#' @importFrom readr read_tsv
#' @importFrom rtracklayer import
#' @import GenomicInteractions
#'
#' @export
makeGenomicInteractionsFromHiCPro <- function(matrixfile,bedfile) {
beddf = rtracklayer::import(bedfile)
matrixdf = read_tsv(matrixfile,col_names=FALSE)
colnames(matrixdf) = c('bini','binj','count')
GenomicInteractions(beddf[matrixdf[['bini']]],beddf[matrixdf[['binj']]],matrixdf[['count']])
}
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