plotSegmentationStates {snapCGH} | R Documentation |
This function displays the estimated hmm states and log2 ratios for each sample.
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)
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 |
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 et.al., JMVA, 2004