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.
MergeSegment            Merge neighboring segments with same somatic
                        copy number and events.
SomatiCA-package        Identifying, characterizing and quantifying
                        somatic copy number aberrations from cancer
                        genome sequencing
SomatiCAFormat-methods
                        ~~ Methods for Function 'SomatiCAFormat' in
                        Package 'SomatiCA' ~~
SomatiCAUsersGuide      View SomatiCA User's Guide
SomatiCApipe            SomatiCA pipeline.
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.
larsCBSsegment          Segmentation based on Circular Binary
                        Segmentation followed by a model selection
                        procedure on detected change points.
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.
somaticRatio            Estimate somatic ratio for given segments.
subclonality            Estimate subclonality for each somatic copy
                        number abberation.
