PureCN (version 1.0.4)

findFocal: Find focal amplifications

Description

Function to find focal amplifications in segmented data. This is automatically called in runAbsoluteCN.

Usage

findFocal(seg, size.cutoff = 2e+06, cn.diff = 2, amp.cutoff = 6)

Arguments

seg

Segmentation data.

size.cutoff

Cutoff for focal in base pairs.

cn.diff

Minimum copy number delta between neighboring segments.

amp.cutoff

Minimum amplification integer copy number.

Value

amplified or not.

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

# The max.candidate.solutions parameter 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,
    args.focal=list(size.cutoff = 2e+06), fun.focal=findFocal)