GenomicReports {beadarraySNP} | R Documentation |
create reports for all samples in a dataset
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"), ...)
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 |
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
Jan Oosting
quantsmooth
,prepareGenomeplot
,
pdfChromosomesSmoothCopyNumber
, pdfSamplesSmoothCopyNumber
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)