segmentExperiment: Segments log2-transformed and GC-adjusted counts.

In cancer-genomics/trellis: Somatic structural variant analysis

Segments log2-transformed and GC-adjusted counts.

Description

Segmentation of the transformed counts is performed by the circular binary segmentation algorithm implemented in the DNAcopy package.

Usage

segmentExperiment(object, tree, param = SegmentParam(), ...)

Arguments

object	A PreprocessViews2 object
tree	A directory tree for storing intermediate files.
param	An object of class SegmentParam.
...	Additional arguments are passed to the segment function in the DNAcopy package.

Value

A GRangesList object. Each element is the set of GRanges for a given sample. Meta-columns of the GRanges elements are seg.mean (the segment mean) and sample (an id for the sample). Note that segmentExperiment saves the GRangesList object as an intermediate file in the provided directory tree. Parameters to the segment function are passed by an instance of the SegmentParam class.

See Also

segment for description of circular binary segmentation and references therein; see SegmentParam-class for a description of the default parameters settings passed to the segment function.

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.