findFocal: Find focal amplifications

View source: R/findFocal.R

findFocalR 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)


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