filterTargets {PureCN} | R Documentation |
This function determines which intervals in the coverage files should be
included or excluded in the segmentation. It is called via the
fun.filterTargets
argument of runAbsoluteCN
. The
arguments are passed via args.filterTargets
.
filterTargets(normal, tumor, log.ratio, seg.file, filter.lowhigh.gc = 0.001, min.coverage = 15, min.targeted.base = 5, normalDB = NULL)
normal |
Coverage data for normal sample. |
tumor |
Coverage data for tumor sample. |
log.ratio |
Copy number log-ratios, one for each target or interval in coverage file. |
seg.file |
If not |
filter.lowhigh.gc |
Quantile q (defines lower q and upper 1-q) for
removing targets with outlier GC profile. Assuming that GC correction might
not have been worked on those. Requires |
min.coverage |
Minimum coverage in both normal and tumor. Targets with
lower coverage are ignored. If a |
min.targeted.base |
Exclude intervals with targeted base (size in bp) smaller than this cutoff. This is useful when the same interval file was used to calculate GC content. For such small targets, the GC content is likely very different from the true GC content of the probes. |
normalDB |
Normal database, created with
|
logical(length(log.ratio))
specifying which targets should be
used in segmentation.
Markus Riester
normal.coverage.file <- system.file("extdata", "example_normal.txt", package="PureCN") normal2.coverage.file <- system.file("extdata", "example_normal2.txt", package="PureCN") normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file) normalDB <- createNormalDatabase(normal.coverage.files) 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, genome="hg19", vcf.file=vcf.file, sampleid="Sample1", interval.file=interval.file, normalDB=normalDB, args.filterTargets=list(min.targeted.base=10), max.ploidy=4, test.purity=seq(0.3,0.7,by=0.05), max.candidate.solutions=1)