plotGoldenGate4OPA {beadarraySNP}R Documentation

Plot Golden Gate genomic view

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


[Package beadarraySNP version 1.58.0 Index]