plotGoldenGate4OPA: Plot Golden Gate genomic view

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

Plots a full genome view based on 4 subsamples of Illumina Golden Gate data

Usage

plotGoldenGate4OPA(object, cn.sum = NULL, sample = 1, plotRaw = FALSE, main = NULL, interact = FALSE, ...)
plotGenomePanels(object, cn.sum = NULL, sample = 1, plotRaw = FALSE, main = NULL, interact = FALSE, allLair=FALSE, panels = list(p1 = c(1, 2, 3, 22), p2 = c(5, 6, 7, 8, 9), p3 = c(10, 11, 12, 13, 14, 15, 21), p4 = c(4, 16, 17, 18, 19, 20, 98, 99)), ...)

Arguments

object	class SnpSetIllumina
cn.sum	list containing genomic states, see createCNSummary
sample	identifier to select the sample within the object
plotRaw	logical, plot raw data points
main	character, Title of plot
interact	logical, plot should be usable for interactive copy number determination interactiveCNselect
allLair	logical, TRUE: plot all LAIR values, FALSE: only plot LAIR values from probes that are heterozygous in the paired normal sample
panels	list, vectors of chromosomes for each panel
...	extra arguments are formwarded to plot

Details

prepare interactive selection

Value

list, see createCNSummary

Author(s)

Jan Oosting

See Also

segmentate, alterCN, interactiveCNselect createCNSummary

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