patchwork.segment: patchwork segmentation function

In xu-chang/patchwork-lite: Allele-specific Copy Number Analysis of whole genome data

Description

Internal function of patchwork.plot().

Usage

patchwork.segment(kbsegs,chroms,Alpha,SD)

Arguments

kbsegs	kbsegs generated from patchwork.smoothing().
chroms	chroms is an object generated from pile.alleles.RData's alf\$achr attribute.
Alpha	Default is inherited from patchwork.plot() and is 0.0001. From DNAcopy (?segment): alpha: significance levels for the test to accept change-points.
SD	Default is inherited from patchwork.plot() and is 1. From DNAcopy (?segment): undo.SD: the number of SDs between means to keep a split if undo.splits="sdundo".

Details

Performs a segmentation using various functions of DNAcopy package and returns the segments in a new object called "segs", saved in Segments.Rdata.

See ?DNAcopy

Author(s)

Markus Mayrhofer, [e-mail] Sebastian DiLorenzo, [e-mail]

See Also

patchwork.plot

xu-chang/patchwork-lite documentation built on May 26, 2019, 6:31 a.m.