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.
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
aCGHfind.hmm.statesplotGenome
Examples
data(colorectal)
plotHmmStates(colorectal, 1)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(aCGH)
Loading required package: cluster
Loading required package: survival
Loading required package: multtest
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'aCGH'
The following object is masked from 'package:stats':
heatmap
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/aCGH/plotHmmStates.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotHmmStates
> ### Title: Plotting the estimated hmm states and log2 ratios for each
> ### sample.
> ### Aliases: plotHmmStates plotHmmStatesNew
> ### Keywords: hplot
>
> ### ** Examples
>
>
> data(colorectal)
> plotHmmStates(colorectal, 1)
>
>
>
>
>
>
> dev.off()
null device
1
>