straw {strawr}

Straw Quick Dump

Description

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(norm, fname, chr1loc, chr2loc, unit, binsize, matrix = "observed")

Arguments

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.

fname

path to .hic file

chr1loc

first chromosome location

chr2loc

second chromosome location

unit

BP (BasePair) or FRAG (FRAGment)

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>.

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.

Details

Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize> [observed/oe/expected]

Value

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)