segment2: A wrapper for DNAcopy's segment function

In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

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

MinimumDistance documentation built on Nov. 8, 2020, 11:11 p.m.