GenomicReports {beadarraySNP}R Documentation

Genomic reports

Description

create reports for all samples in a dataset

Usage

reportChromosomesSmoothCopyNumber(snpdata, grouping, normalizedTo = 2, 
  smooth.lambda = 2, ridge.kappa = 0, plotLOH = c("none", "marker", "line", "NorTum"), ...)
reportSamplesSmoothCopyNumber(snpdata, grouping, normalizedTo = 2, 
  smooth.lambda = 2, ridge.kappa = 0, plotLOH = c("none", "marker", "line", "NorTum"), ...)

Arguments

snpdata SnpSetIllumina object
grouping factor, elements with same value are plotted together. Defaults to groups of 4 in order of the samples in the object
normalizedTo numeric, a horizontal line is drawn at this position
smooth.lambda smoothing parameter for quantsmooth
ridge.kappa smoothing parameter for quantsmooth
plotLOH indicate regions or probes with LOH, see details
... arguments are forwarded to plot

Details

The first function creates plots for each group and each chromosome in the dataset. The second function creates full genome plot for each group in the dataset. Beware that a lot of plots can be created, and usually you should prepare for that, by redirecting the plots to pdf or functions that create picture files like jpg, png, bmp

Value

Author(s)

Jan Oosting

See Also

quantsmooth,prepareGenomeplot, pdfChromosomesSmoothCopyNumber, pdfSamplesSmoothCopyNumber

Examples

data(chr17.260)
chr17nrm<-standardNormalization(chr17.260)
par(mfrow=c(4,2),mar=c(2,4,2,1))
reportChromosomesSmoothCopyNumber(chr17nrm, grouping=pData(chr17.260)$Group,smooth.lambda = 4)

[Package beadarraySNP version 1.0.0 Index]