segment2: A wrapper for DNAcopy's segment function

Description Usage Arguments See Also

Description

Methods for circular binary segmentation.

Usage

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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


Bioconductor-mirror/MinimumDistance documentation built on July 1, 2017, 5:19 a.m.