R/RcppExports.R

In strawr: Fast Implementation of Reading/Dump for .hic Files

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#' Straw Quick Dump
#'
#' fast C++ implementation of dump. Not as fully featured as the
#' Java version. Reads the .hic file, finds the appropriate matrix and slice
#' of data, and outputs as data.frame in sparse upper triangular format.
#' Currently only supporting matrices.
#'
#' Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize> [observed/oe/expected]
#'
#' @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 fname path to .hic file
#' @param chr1loc first chromosome location
#' @param chr2loc second chromosome location
#' @param unit BP (BasePair) or FRAG (FRAGment)
#' @param binsize 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>.
#' @param matrix Type of matrix to output. Must be one of observed/oe/expected.
#'     observed is observed counts, oe is observed/expected counts, expected is expected counts.
#' @return Data.frame of a sparse matrix of data from hic file. x,y,counts
#' @examples
#' straw("NONE", system.file("extdata", "test.hic", package = "strawr"), "1", "1", "BP", 2500000)
#' @export
straw <- function(norm, fname, chr1loc, chr2loc, unit, binsize, matrix = "observed") {
    .Call('_strawr_straw', PACKAGE = 'strawr', norm, fname, chr1loc, chr2loc, unit, binsize, matrix)
}

#' Function for reading chromosomes from .hic file
#'
#' @param fname path to .hic file
#' @return Data frame of chromosome names and lengths
#' @examples
#' readHicChroms(system.file("extdata", "test.hic", package = "strawr"))
#' @export
readHicChroms <- function(fname) {
    .Call('_strawr_readHicChroms', PACKAGE = 'strawr', fname)
}

#' Function for reading basepair resolutions from .hic file
#'
#' @param fname path to .hic file
#' @return Vector of basepair resolutions
#' @examples
#' readHicBpResolutions(system.file("extdata", "test.hic", package = "strawr"))
#' @export
readHicBpResolutions <- function(fname) {
    .Call('_strawr_readHicBpResolutions', PACKAGE = 'strawr', fname)
}

#' Function for reading available normalizations from .hic file
#' 
#' @param fname path to .hic file
#' @return Vector of available normalizations
#' @examples
#' readHicNormTypes(system.file("extdata", "test.hic", package = "strawr"))
#' @export
readHicNormTypes <- function(fname) {
    .Call('_strawr_readHicNormTypes', PACKAGE = 'strawr', fname)
}