R/RcppExports.R

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' straw
#'
#' Adapted C++ implementation of Juicer's dump. Reads the .hic file, finds the
#' appropriate matrix and slice of data, and outputs as an R DataFrame.
#' 
#' Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>
#' 
#' @importFrom Rcpp sourceCpp
#' @param norm Normalization to apply. Must be one of NONE/VC/VC_SQRT/KR.
#'     VC is vanilla coverage, VC_SQRT is square root of vanilla coverage,
#'     and KR is Knight-Ruiz or Balanced normalization.
#' @param fn path to the .hic file
#' @param ch1 first chromosome location (e.g., "1")
#' @param ch2 second chromosome location (e.g., "8")
#' @param u BP (BasePair) or FRAG (restriction enzyme FRAGment)
#' @param bs The bin size. By default, for BP, this is one of 
#'     <2500000, 1000000, 500000,
#'     250000, 100000, 50000, 25000, 10000, 5000> and for FRAG this is one of 
#'     <500, 200,
#'     100, 50, 20, 5, 2, 1>.
#' @return Data.frame of a sparse matrix of data from hic file. x,y,counts
straw <- function(norm, fn, ch1, ch2, u, bs) {
    .Call(`_HiCDCPlus_straw`, norm, fn, ch1, ch2, u, bs)
}