straw {HiCDCPlus} | R Documentation

## straw

### Description

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(norm, fn, ch1, ch2, u, bs)

### 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.
`fn` | path to the .hic file
`ch1` | first chromosome location (e.g., "1")
`ch2` | second chromosome location (e.g., "8")
`u` | BP (BasePair) or FRAG (restriction enzyme FRAGment)
`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>.

### Details

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

### Value

Data.frame of a sparse matrix of data from hic file. x,y,counts

[Package HiCDCPlus version 1.0.0 Index]