segmentationPSCBS {PureCN} | R Documentation

## PSCBS segmentation

### Description

Alternative segmentation function using the `PSCBS` package. This function is called via the `fun.segmentation` argument of `runAbsoluteCN`. The arguments are passed via `args.segmentation`.

### Usage

    segmentationPSCBS(
      normal,
      tumor,
      log.ratio,
      seg,
      plot.cnv,
      sampleid,
      weight.flag.pvalue = 0.01,
      alpha = 0.005,
      undo.SD = NULL,
      flavor = "tcn&dh",
      tauA = 0.03,
      vcf = NULL,
      tumor.id.in.vcf = 1,
      normal.id.in.vcf = NULL,
      max.segments = NULL,
      boost.on.target.max.size = 30,
      prune.hclust.h = NULL,
      prune.hclust.method = "ward.D",
      chr.hash = NULL,
      centromeres = NULL,
      ...
    )

### Arguments

`normal` | Coverage data for normal sample.
`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.
`plot.cnv` | Segmentation plots.
`sampleid` | Sample id, used in output files.
`weight.flag.pvalue` | Flag values with one-sided p-value smaller than this cutoff.
`alpha` | Alpha value for CBS, see documentation for the `segment` function.
`undo.SD` | `undo.SD` for CBS, see documentation of the `segment` function. If `NULL`, try to find a sensible default.
`flavor` | Flavor value for PSCBS. See `segmentByNonPairedPSCBS`.
`tauA` | tauA argument for PSCBS. See `segmentByNonPairedPSCBS`.
`vcf` | Optional VCF 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. If `NULL`, use unpaired PSCBS.
`max.segments` | If not `NULL`, try a higher `undo.SD` parameter if number of segments exceeds the threshold.
`boost.on.target.max.size` | When off-target regions are noisy compared to on-target, try to find small segments of specified maximum size that might be missed to due the increased noise. Set to 0 to turn boosting off.
`prune.hclust.h` | Height in the `hclust` pruning step. Increasing this value will merge segments more aggressively. If `NULL`, try to find a sensible default.
`prune.hclust.method` | Cluster method used in the `hclust` pruning step. See documentation for the `hclust` function.
`chr.hash` | Mapping of non-numerical chromsome names to numerical names (e.g. chr1 to 1, chr2 to 2, etc.). If `NULL`, assume chromsomes are properly ordered.
`centromeres` | A `GRanges` with centromere positions. If not `NULL`, add breakpoints at centromeres.
`...` | Additional parameters passed to the `segmentByNonPairedPSCBS` function.

### Value

`data.frame` containing the segmentation.

### Author(s)

Markus Riester

### References

Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.

Venkatraman, E. S., Olshen, A. B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-63.

Olshen et al. (2011). Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics.

### 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.
     ret <-runAbsoluteCN(normal.coverage.file=normal.coverage.file,
         tumor.coverage.file=tumor.coverage.file, vcf.file=vcf.file,
         sampleid="Sample1",  genome="hg19",
         fun.segmentation=segmentationPSCBS, max.ploidy=4,
         test.purity=seq(0.3,0.7,by=0.05), max.candidate.solutions=1)

[Package PureCN version 1.20.0 Index]