PureCN (version 1.0.3)

segmentationPSCBS: PSCBS segmentation

Description

Segmentation function. Uses the PSCBS package. This function is called via the fun.segmentation argument of runAbsoluteCN. The arguments are passed via args.segmentation.

Usage

segmentationPSCBS(normal, tumor, log.ratio, plot.cnv, 
    coverage.cutoff, sampleid = sampleid, exon.weight.file = NULL, 
    flavor = "tcn&dh", tauA = 0.03, 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. NOT SUPPORTED YET.

flavor

Flavor value for PSBCS. See segmentByNonPairedPSCBS.

tauA

tauA argument for PSCBS. See segmentByNonPairedPSCBS.

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.

...

Additional parameters passed to the segmentByNonPairedPSCBS function.

Value

• A list with elements seg and size. "seg" contains 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")

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, fun.segmentation=segmentationPSCBS)