findFocal: Find focal amplifications

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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)

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.