PureCN (version 1.0.3)

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

• Boolean vector for each segment wether it is focally 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)