PureCN (version 1.0.3)

segmentationCBS: CBS segmentation

Description

The default segmentation function. This function is called via the fun.segmentation argument of runAbsoluteCN. The arguments are passed via args.segmentation.

Usage

segmentationCBS(normal, tumor, log.ratio, plot.cnv, 
    coverage.cutoff, sampleid = sampleid, exon.weight.file = NULL, 
    alpha = 0.005, vcf = NULL, tumor.id.in.vcf = 1, 
    verbose = TRUE)

Arguments

normal

GATK coverage data for normal sample.

tumor

GATK coverage data for tumor sample.

log.ratio

Copy number log-ratios, one for each exon in coverage file.

plot.cnv

Segmentation plots.

coverage.cutoff

Minimum coverage in both normal and tumor.

sampleid

Sample id, used in output files.

exon.weight.file

Can be used to assign weights to exons.

alpha

Alpha value for CBS, see documentation for the segment function.

vcf

Optional VCF object with germline allelic ratios.

tumor.id.in.vcf

Id of tumor in case multiple samples are stored in VCF.

verbose

Verbose output.

Value

• A list with elements
• seg
  The segmentation.
• size
  The size of all segments (in base pairs).

Examples

gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")
vcf.file <- system.file("extdata", "example_vcf.vcf", 
    package="PureCN")
gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt", 
    package="PureCN")

# speed-up the runAbsoluteCN by using the stored grid-search.
# (purecn.example.output$candidates).
data(purecn.example.output)

# The max.candidate.solutions argument is set to a very low value only to 
# speed-up this example. This is not a good idea for real samples.
ret <-runAbsoluteCN(gatk.normal.file=gatk.normal.file, 
    gatk.tumor.file=gatk.tumor.file, 
    vcf.file=vcf.file, sampleid='Sample1', gc.gene.file=gc.gene.file, 
    candidates=purecn.example.output$candidates, max.candidate.solutions=2,
    fun.segmentation=segmentationCBS, args.segmentation=list(alpha=0.001))