segmentationGATK4 {PureCN} | R Documentation

## 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)

[Package PureCN version 2.0.2 Index]