R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(QDNAseq)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/QDNAseq/frequencyPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: frequencyPlot
> ### Title: Plot copy number aberration frequencies
> ### Aliases: frequencyPlot frequencyPlot,QDNAseqCopyNumbers,missing-method
> ### Keywords: hplot
>
> ### ** Examples
>
> data(LGG150)
> readCounts <- LGG150
> readCountsFiltered <- applyFilters(readCounts)
38,819 total bins
38,819 of which in selected chromosomes
36,722 of which with reference sequence
33,347 final bins
> readCountsFiltered <- estimateCorrection(readCountsFiltered)
Calculating correction for GC content and mappability
Calculating fit for sample LGG150 (1 of 1) ...
Done.
> copyNumbers <- correctBins(readCountsFiltered)
> copyNumbersNormalized <- normalizeBins(copyNumbers)
Applying median normalization ...
> copyNumbersSmooth <- smoothOutlierBins(copyNumbersNormalized)
Smoothing outliers ...
> copyNumbersSegmented <- segmentBins(copyNumbersSmooth)
Performing segmentation:
Segmenting: LGG150 (1 of 1) ...
> copyNumbersSegmented <- normalizeSegmentedBins(copyNumbersSegmented)
> copyNumbersCalled <- callBins(copyNumbersSegmented)
EM algorithm started ...
[1] "Total number of segments present in the data: 16"
[1] "Number of segments used for fitting the model: 13"
21260653048817113.623.332054524701432171.235.924955904669738133.335.7
Calling iteration1:
optim results
time: 1
minimum: 16440.1358811675
116440.1156813435-1.11506058878143-0.6511447768520950.001148304813960850.3075292319462840.5257246944328131.040782914303450.161094049715017-0.01913116657745530.0193307990291194-0.0397793945356270.07730294582386270.196802474074343
21271623050489113.723.332054524701432171.235.932054524669738171.235.7
Calling iteration2:
optim results
time: 0
minimum: 16440.087930575
116439.9749789855-1.05479070177207-0.651452243764630.0003129552409922090.3188930618887660.5451512900324841.060336867134650.140015863961494-0.01881944629335520.018961062084617-0.0390095348884650.04655236735530310.17630808675607
EM algorithm done ...
Computing posterior probabilities for all segments ...
Total time:0minutes
Adjusting segmented data for cellularity ...
Cellularity sample1: 1
Adjusting normalized data for cellularity ...
Cellularity sample1: 1
1
21288053283236113.725.132054525721718171.243.732054524669738171.235.7
21288193449981113.726.432054525721718171.243.732054525710228171.243.6
21288173449976113.726.432054525721718171.243.732054525710228171.243.6
21288503783750113.728.932054525721718171.243.732054525710228171.243.6
21292103717675113.828.432054525721718171.243.732054525710228171.243.6
21292153717677113.828.432054525721718171.243.732054525710228171.243.6
21292213717680113.828.432054525721718171.243.732054525710228171.243.6
21292273717683113.828.432054525721718171.243.732054525710228171.243.6
21292333717686113.828.432054525721718171.243.732054525710228171.243.6
21292363717689113.828.432054525721718171.243.732054525710228171.243.6
21292543817765113.829.232054525721718171.243.732054525710228171.243.6
21296813817937113.829.232054525721718171.243.732054525710228171.243.6
FINISHED!
Total time:0minutes
> frequencyPlot(copyNumbersCalled)
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> dev.off()
null device
1
>