plotHmmStates {aCGH}R Documentation

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


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


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


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


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.


Jane Fridlyand


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

See Also

aCGH find.hmm.states plotGenome


plotHmmStates(colorectal, 1)

[Package aCGH version 1.1.4 Index]