beadarraySNP (version 1.38.0)

GenomicReports: 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"),  sample.colors = NULL, ideo.bleach=0.25, ...)
reportSamplesSmoothCopyNumber(snpdata, grouping, normalizedTo=2,  smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"),  sample.colors=NULL, ...)
reportGenomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, sizeSampleNames=4,  distance.min, upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey",  lohwidth=1, segment=101, orientation=c("V","H"), ...)
reportChromosomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, distance.min, upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey", proportion=0.2,  plotLOH=TRUE, segment=101, ...)
reportGenomeIntensityPlot(snpdata, normalizedTo=NULL, subsample=NULL, smoothing=c("mean", "quant"), dot.col="black", smooth.col="red", ...)

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.

sample.colors

vector of color.

plotSampleNames

logical.

sizeSampleNames

numeric, margin size for sample names.

distance.min

numerical.

upcolor

color.

downcolor

color.

lohcolor

color.

hetcolor

color.

lohwidth

numerical, relative width of the LOH part of the sample

segment

integer.

orientation

["V","H"], vertical or horizontal orientation of plot.

proportion

numerical, proportion of the plot to use for idiogram annotation

subsample

character, or factor of length of features

smoothing

Type of smoothing per chromosome.

dot.col

color.

smooth.col

color.

ideo.bleach

numeric [0,1]

...

arguments are forwarded to plot or getChangedRegions.

Value

These functions are executed for their side effects

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.

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)