extractHiC: extracts HiC data from .hic file using Straw
In PhanstielLab/SushiRoll: Genome plotting with grid Graphics

Description Usage Arguments

View source: R/extractHiC.R

extracts HiC data from .hic file using Straw

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extractHiC(hic, format, chrom, chromstart = NULL, chromend = NULL,
  resolution, zrange = NULL, norm = "NONE", resscale = "BP",
  altchrom = NULL, altchromstart = NULL, altchromend = NULL)

`hic`	path to .hic file
`format`	format of data wanted, which will depend on what kind of plot is ultimately desired; options are "sparse" and "full"
`chrom`	if not alternative chromosome, chromosome of desired region
`chromstart`	chromosome start position of chrom, in bp
`chromend`	chromosome end position of chrom, in bp
`resolution`	the width in bp of each pixel
`zrange`	the range of interaction scores to plot, where extreme values will be set to the max or min
`norm`	hic data normalization; options are "NONE", "VC", "VC_SQRT", and "KR"
`resscale`	scale of normalization; options are "BP" and "FRAG"
`altchrom`	if looking at region between two different chromosomes, this is the specified alternative chromsome
`altchromstart`	if looking at region between two different chromosomes, start position of altchrom
`altchromend`	if looking at region between two different chromsomes, end position of altchrom