SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing


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Documentation for package ‘SomatiCA’ version 1.6.0

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SomatiCA-package Identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing
admixtureRate Estimate the admixture rate of normal cells in a tumor sample.
collapse Collapse measurements with a certain bin size.
copynumberCorrected Somatic copy number corrected by admixture rate.
denoise Smoothing procedure by replacing outliers.
GCbiasRemoval Correct GC bias for read depth ratio of each site.
GCcontent GC content for hg19 human genome at each 1Mb interval.
GCcount Calculate the GC content of given window size for a chromosome.
larsCBSsegment Segmentation based on Circular Binary Segmentation followed by a model selection procedure on detected change points.
MergeSegment Merge neighboring segments with same somatic copy number and events.
plotSegment Plot segmentation.
plotSubclonality Plot clonality and somatic copy number.
refineSegment Refine the segmentation based on estimated somatic ratio.
segmentGCbiasRemoval Correct GC bias for read depth ratio of each segment.
segwithratio Segments with somatic ratio.
SomatiCA Identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing
SomatiCAFormat ~~ Methods for Function 'SomatiCAFormat' in Package 'SomatiCA' ~~
SomatiCAFormat-method ~~ Methods for Function 'SomatiCAFormat' in Package 'SomatiCA' ~~
SomatiCAFormat-methods ~~ Methods for Function 'SomatiCAFormat' in Package 'SomatiCA' ~~
SomatiCApipe SomatiCA pipeline.
SomatiCAUsersGuide View SomatiCA User's Guide
somaticRatio Estimate somatic ratio for given segments.
subclonality Estimate subclonality for each somatic copy number abberation.