GenomicReports: Genomic reports

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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.

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

These functions are executed for their side effects

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)

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