kataegis: Calculate regions of kataegis from a VCF file.
In jjellis/GenomicVis: Genomic Visualisation Routines

Description Usage Arguments Details Value Author(s) Examples

Identify regions of kataegis. The input GRanges instance should only contain SNV (i.e., no INDELs) that have a single ALT allele. The input GRanges instance must also contain a valid Seqinfo class that gives the lengths of the chromosomes. The easiest way to obtain this from a VCF file is via the read.vcf function from this package.

1 2	kataegis(x, min.snvs = 6, max.mean.distance = 1000, pcf = FALSE, maxseg = NA, maxk = NA, ncpus = getOption("cl.cores", 1))

`x`	A `GRanges` instance containing SNVs.
`min.snvs`	the minimum number of SNVs in a kataegis region
`max.mean.distance`	the minimum mean genetic distance in a kataegis region.
`pcf`	Use piece-wise constant curve fitting algorithm to identify kataegis. See 'Details' below.
`maxseg`	maximum segments in PCF algorithm, see Details.
`maxk`	maximum length of segments in PCF algorithm, see Details.
`ncpus`	Run the function in parallel using this number of CPUs.

Details ...

A GRanges object representing the regions of kataegis identified

Jonathan Ellis <jonathan.j.ellis@gmail.com>

## Not run: 
vcf.file <- system.file('extdata', 'example.vcf',
  package = 'GenomicVis')
vcf <- read.vcf(vcf.file, 'GRCh37')
x <- rowData(vcf)
kat <- kataegis(x)

## End(Not run)