heatmap
(Package: aCGH) :
Creates heatmap array CGH objects
Clusters samples and produces heatmapp of the observed log2ratios.
● Data Source:
BioConductor
● Keywords: cluster, hplot
● Alias: heatmap
●
2 images
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impute.HMM
(Package: aCGH) :
Imputing log2 ratios using HMM
Imputing log2 ratios using the output of the HMM segmenttation
● Data Source:
BioConductor
● Keywords: models
● Alias: impute.HMM
●
0 images
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impute.lowess
(Package: aCGH) :
Imputing log2 ratios
Imputing log2 ratios
● Data Source:
BioConductor
● Keywords: models
● Alias: impute.lowess
●
0 images
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mergeFunc
(Package: aCGH) :
Funtion to merge states based on their state means
mergeFunc takes the output of hmm.run.func (or find.hmm.states) with a particular model selection criterion and iteratively merges the states with means closer than a supplied threshold. mergeHmmStates is a frontend for mergeFunc using aCGH object.
● Data Source:
BioConductor
● Keywords: models
● Alias: mergeFunc, mergeHmmStates
●
0 images
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Merging of predicted levels for array CGH data and similar.
● Data Source:
BioConductor
● Keywords: htest
● Alias: combine.func, mergeLevels
●
1 images
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plotFreqStat
(Package: aCGH) :
frequency plots and significance analysis
The main application of this function is to plot the frequency of changes.
● Data Source:
BioConductor
● Keywords: hplot, htest
● Alias: plotFreqStat
●
3 images
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plotGenome
(Package: aCGH) :
Plots the genome
Basic plot of the log2 ratios for each array ordered along the genome.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: maPalette, plotCGH.func, plotGene, plotGeneSign, plotGenome
●
0 images
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This function displays the estimated hmm states and log2 ratios for each sample.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: plotHmmStates, plotHmmStatesNew
●
23 images
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This function display the genomic events and tests for the differences between groups if they are specified.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: plotSummaryProfile
●
9 images
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states.hmm.func
(Package: aCGH) :
A function to fit unsupervised Hidden Markov model
This function is a workhorse of find.hmm.states. It operates on the individual chromosomes/samples and is not called directly by users.
● Data Source:
BioConductor
● Keywords: models
● Alias: states.hmm.func
●
0 images
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providing 
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