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

## Documentation for package ‘SomatiCA’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.