segmentationGATK4: GATK4 ModelSegments segmentation function

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

GATK4 ModelSegments segmentation function

Description

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.

Usage

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,
  ...
)

Arguments

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 CollapsedVCF object with germline allelic ratios.
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 --number-of-changepoints-penalty-factor. If NULL, find a sensible default. Ignored when provided in additional.cmd.args.
additional.cmd.args	character(1). By default, ModelSegments is called with default parameters. Provide additional arguments here.
chr.hash	Not needed here since ModelSegments does not require numbered chromosome names.
...	Currently unused arguments provided to other segmentation functions.

Value

data.frame containing the segmentation.

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")

# 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)

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