SomatiCA is a software suite that is capable of identifying, characterizing, and quantifying somatic CNAs from cancer genome sequencing. First, it uses read depths and lesser allele frequencies (LAF) from mapped short sequence reads to segment the genome and identify candidate CNAs. Second, SomatiCA estimates the admixture rate from the relative copy-number profile of tumor-normal pair by a Bayesian finite mixture model. Third, SomatiCA quantifies absolute somatic copy-number and subclonality for each genomic segment to guide its characterization. Results from SomatiCA can be further integrated with single nucleotide variations (SNVs) to get a better understanding of the tumor evolution.
|Author||Mengjie Chen <email@example.com>, Hongyu Zhao <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Mengjie Chen <email@example.com>|
admixtureRate: Estimate the admixture rate of normal cells in a tumor...
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...
larsCBSsegment: Segmentation based on Circular Binary Segmentation followed...
MergeSegment: Merge neighboring segments with same somatic copy number and...
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.
SomatiCAFormat-methods: ~~ Methods for Function 'SomatiCAFormat' in Package...
SomatiCA-package: Identifying, characterizing and quantifying somatic copy...
SomatiCApipe: SomatiCA pipeline.
SomatiCAUsersGuide: View SomatiCA User's Guide
somaticRatio: Estimate somatic ratio for given segments.
subclonality: Estimate subclonality for each somatic copy number...