| findFocal {PureCN} | R Documentation |
Function to find focal amplifications in segmented data. This is
automatically called in runAbsoluteCN.
findFocal(seg, max.size = 3e+06, cn.diff = 2, min.amp.cn = 5)
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. |
logical(n), indicating for all n segments whether they are
focally amplified or not.
Markus Riester
normal.coverage.file <- system.file("extdata", "example_normal.txt",
package="PureCN")
tumor.coverage.file <- system.file("extdata", "example_tumor.txt",
package="PureCN")
vcf.file <- system.file("extdata", "example_vcf.vcf.gz",
package="PureCN")
interval.file <- system.file("extdata", "example_intervals.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)