aCGH (version 1.50.0)

plotHmmStates: 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

plotHmmStates(aCGH.obj, sample.ind, chr = 1:num.chromosomes(aCGH.obj), statesres = hmm.merged(aCGH.obj), maxChrom = 23, chrominfo = human.chrom.info.Jul03, yScale = c(-2, 2), samplenames = sample.names(aCGH.obj))

Arguments

aCGH.obj

object of class aCGH

sample.ind

index of the sample to be plotted relative to the data matrix (i.e. column index in the file)

statesres

matrix containing states informations. defaults to the states selected using the first model selection criterionof aCGH.obj

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

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.

References

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

See Also

aCGH find.hmm.states plotGenome

Examples

data(colorectal)
plotHmmStates(colorectal, 1)