segmentationGATK4 {PureCN} | R Documentation |
A wrapper for GATK4s ModelSegmentation function, useful when normalization
is performed with other tools than GATK4, for example PureCN.
This function is called via the
fun.segmentation
argument of runAbsoluteCN
. The
arguments are passed via args.segmentation
.
segmentationGATK4( normal, tumor, log.ratio, seg, vcf = NULL, tumor.id.in.vcf = 1, normal.id.in.vcf = NULL, min.logr.sdev = 0.15, prune.hclust.h = NULL, prune.hclust.method = NULL, changepoints.penality = NULL, additional.cmd.args = "", chr.hash = NULL, ... )
normal |
Coverage data for normal sample. Ignored in this function. |
tumor |
Coverage data for tumor sample. |
log.ratio |
Copy number log-ratios, one for each exon in coverage file. |
seg |
If segmentation was provided by the user, this data structure will contain this segmentation. Useful for minimal segmentation functions. Otherwise PureCN will re-segment the data. This segmentation function ignores this user provided segmentation. |
vcf |
Optional |
tumor.id.in.vcf |
Id of tumor in case multiple samples are stored in VCF. |
normal.id.in.vcf |
Id of normal in in VCF. Currently not used. |
min.logr.sdev |
Minimum log-ratio standard deviation used in the model. Useful to make fitting more robust to outliers in very clean data. |
prune.hclust.h |
Ignored in this function. |
prune.hclust.method |
Ignored in this function. |
changepoints.penality |
The |
additional.cmd.args |
|
chr.hash |
Not needed here since |
... |
Currently unused arguments provided to other segmentation functions. |
data.frame
containing the segmentation.
Markus Riester
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") # 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. ## Not run: ret <-runAbsoluteCN(normal.coverage.file=normal.coverage.file, tumor.coverage.file=tumor.coverage.file, vcf.file=vcf.file, sampleid="Sample1", genome="hg19", fun.segmentation = segmentationGATK4, max.ploidy=4, args.segmentation = list(additional.cmd.args = "--gcs-max-retries 19"), test.purity=seq(0.3,0.7,by=0.05), max.candidate.solutions=1) ## End(Not run)