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 1.52.0 Index]