segment2 {MinimumDistance} | R Documentation

## A wrapper for DNAcopy's segment function

### Description

Methods for circular binary segmentation.

### Usage

    segment2(object, ...)

    ## S4 method for signature 'TrioSet'
    segment2(object, md = NULL, segmentParents = TRUE, verbose = TRUE, ...)

    ## S4 method for signature 'matrix'
    segment2(object, pos, chrom, id, featureNames, ...)

    ## S4 method for signature 'ff_matrix'
    segment2(object, pos, chrom, id, featureNames, ...)

    ## S4 method for signature 'arrayORff_array'
    segment2(
      object,
      pos,
      chrom,
      id,
      featureNames,
      segmentParents = TRUE,
      verbose = TRUE,
      ...
    )

### Arguments

`object` | see `showMethods{segment2}`
`...` | Additional arguments passed to DNAcopy's `segment`.
`md` | a matrix of the minimum distance
`segmentParents` | logical. Whether to segment the log R ratios of the parents using circular binary segmentation.
`verbose` | logical. Whether to display messages that indicate progress.
`pos` | integer vector of physical position of markers in the genome
`chrom` | character or integer vector of chromosome names
`id` | character vector of trio identifiers for subsetting `object`
`featureNames` | character vector specifying marker names for subsetting `object`

### See Also

`segment`

`segment`

[Package MinimumDistance version 1.31.1 Index]