createCNSummary: Summarization of Copy number states

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

Create a summary object of the genomic copy number states in a sample of segmented data

Usage

createCNSummary(object, sample, dnaIndex=1, subsample = "OPA")

Arguments

object	SNPSetIllumina object after segmentation segmentate
sample	SampleName or index of the sample for which to create the summary
dnaIndex	Measured DNA index of the sample
subsample	factor or column name in featureData slot

Details

The segments within a sample are assigned a copy number value. When the inferred slot in assayData is empty, all segments will be set to 2. Otherwise the values are recovered from the inferred slot. Gender is taken into account for the sex chromosomes.

Value

list with the following elements

dnaIndex	same as parameter dnaIndex
CN.total.nrm	Total expected copynumber for a 'normal' specimen ~ 2*featurecount
states	data.frame with columns opa, count ,intensity, copynumber

This list can be used as the cn.sum argument for plotGoldenGate4OPA, alterCN, getDNAindex and setRealCN

Author(s)

Jan Oosting

See Also

segmentate, alterCN, plotGoldenGate4OPA

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