plotSegmentationStates {snapCGH}R Documentation

Plotting the estimated hmm states and log2 ratios for each sample.

Description

This function displays the estimated hmm states and log2 ratios for each sample.

Usage


plotSegmentationStates(segList, geList, array=1, chr = 1:length(unique(segList$genes$Chr)), maxChrom = 22,
                 chrominfo = chrominfo.Mb, yScale = c(-2, 2),
                 samplenames = colnames(segList), xlower = 0,
                 xupper = chrominfo$length[chr[j]]/1000)

Arguments

segList object of class SegList
geList object of class GEList
array index of the array to be plotted
chr vector of chromosomes to be plotted
yScale specified scale for Y-exis
maxChrom highest chromosome to show
chrominfo a chromosomal information associated with the mapping of the data
samplenames vector of sample names
xlower integer value specifying the lower limit of the x-axis
xupper integer value specifying the upper limit of the x-axis

Details

Each chromosome is plotted on a separate page and contains two figures. The top figure shows the observed log2ratios and the bottom figure shows predicted values for all clones but outliers which show observed values. The genomic events are indicated on both figures as following. The first clone after transition is indicated with solid blue line and the last clone after transitions is shown with dotted green line. Focal aberrations clones are colored orange, amplifications are colored red and outliers are yellow.

Author(s)

Jane Fridlyand

References

Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004

See Also

SegList runHomHMM genomePlot

Examples



[Package snapCGH version 1.0.0 Index]