findFocal {PureCN} | R Documentation

## Find focal amplifications

### Description

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

### Usage

    findFocal(seg, max.size = 3e+06, cn.diff = 2, min.amp.cn = 5)

### Arguments

`seg` | Segmentation data.
`max.size` | Cutoff for focal in base pairs.
`cn.diff` | Minimum copy number delta between neighboring segments.
`min.amp.cn` | Minimum amplification integer copy number. Segments with lower copy number are not tested.

### Value

`logical(n)`, indicating for all n segments whether they are focally amplified or not.

### Author(s)

Markus Riester

### See Also

`runAbsoluteCN`

### Examples

    normal.coverage.file <- system.file("extdata", "example_normal_tiny.txt",
        package="PureCN")
    tumor.coverage.file <- system.file("extdata", "example_tumor_tiny.txt",
        package="PureCN")
    vcf.file <- system.file("extdata", "example.vcf.gz",
        package="PureCN")
    interval.file <- system.file("extdata", "example_intervals_tiny.txt",
        package="PureCN")

    # The max.candidate.solutions, max.ploidy and test.purity parameters are set to
    # non-default values to speed-up this example.  This is not a good idea for real
    # samples.
    ret <-runAbsoluteCN(normal.coverage.file=normal.coverage.file,
        tumor.coverage.file=tumor.coverage.file, vcf.file=vcf.file, genome="hg19",
        sampleid="Sample1", interval.file=interval.file,
        max.candidate.solutions=1, max.ploidy=4, test.purity=seq(0.3,0.7,by=0.05),
        args.focal=list(max.size = 2e+06), fun.focal=findFocal)

[Package PureCN version 1.14.3 Index]