interactiveCNselect: Interactive assignment of copynumbers to genomic segments

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

This function plots the genomic view of a sample, and allows the assignment of a discrete copy number to each segment

Usage

interactiveCNselect(object, sample = 1, dnaIndex)

Arguments

object	class SnpSetIllumina after segmentation
sample	Sample identifier within object
dnaIndex	numeric, measured DNA index of the sample (1=normal)

Details

The user can interactively assign discrete, integer copy number values to each segment. This is done by either clicking in the lower part of a panel to decrease the copy number, or in the higher part of a panel to increase the copy number. The order of copy number values is always maintained; a segment with a lower raw value can not get a higher copy number assigned then a segment with a higher raw copy number value.

Value

list, see createCNSummary

Author(s)

Jan Oosting

See Also

segmentate, alterCN, plotGoldenGate4OPA createCNSummary

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.