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

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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 <mengjie.chen@yale.edu>, Hongyu Zhao <hongyu.zhao@yale.edu>
Date of publication
None
Maintainer
Mengjie Chen <mengjie.chen@yale.edu>
License
GPL (>=2)
Version
2.2.1

View on Bioconductor

Man pages

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...

Files in this package

SomatiCA/DESCRIPTION
SomatiCA/NAMESPACE
SomatiCA/R
SomatiCA/R/AllGeneric.R
SomatiCA/R/GCbiasRemoval.R
SomatiCA/R/GCcount.R
SomatiCA/R/MergeSegment.R
SomatiCA/R/SomatiCA-internal.R
SomatiCA/R/SomatiCAFormat.R
SomatiCA/R/SomatiCAUsersGuide.R
SomatiCA/R/SomatiCApipe.R
SomatiCA/R/admixtureRate.R
SomatiCA/R/collapse.R
SomatiCA/R/copynumberCorrected.R
SomatiCA/R/denoise.R
SomatiCA/R/larsCBSsegment.R
SomatiCA/R/plotSegment.R
SomatiCA/R/plotSubclonality.R
SomatiCA/R/refineSegment.R
SomatiCA/R/segmentGCbiasRemoval.R
SomatiCA/R/somaticRatio.R
SomatiCA/R/subclonality.R
SomatiCA/R/zzz.R
SomatiCA/build
SomatiCA/build/vignette.rds
SomatiCA/data
SomatiCA/data/GCcontent.rda
SomatiCA/data/datalist
SomatiCA/data/segwithratio.rda
SomatiCA/inst
SomatiCA/inst/CITATION
SomatiCA/inst/doc
SomatiCA/inst/doc/SomatiCA.R
SomatiCA/inst/doc/SomatiCA.Rnw
SomatiCA/inst/doc/SomatiCA.pdf
SomatiCA/inst/doc/SomatiCAUserGuide.pdf
SomatiCA/man
SomatiCA/man/GCbiasRemoval.Rd
SomatiCA/man/GCcontent.Rd
SomatiCA/man/GCcount.Rd
SomatiCA/man/MergeSegment.Rd
SomatiCA/man/SomatiCA-package.Rd
SomatiCA/man/SomatiCAFormat-methods.Rd
SomatiCA/man/SomatiCAUsersGuide.Rd
SomatiCA/man/SomatiCApipe.Rd
SomatiCA/man/admixtureRate.Rd
SomatiCA/man/collapse.Rd
SomatiCA/man/copynumberCorrected.Rd
SomatiCA/man/denoise.Rd
SomatiCA/man/larsCBSsegment.Rd
SomatiCA/man/plotSegment.Rd
SomatiCA/man/plotSubclonality.Rd
SomatiCA/man/refineSegment.Rd
SomatiCA/man/segmentGCbiasRemoval.Rd
SomatiCA/man/segwithratio.Rd
SomatiCA/man/somaticRatio.Rd
SomatiCA/man/subclonality.Rd
SomatiCA/vignettes
SomatiCA/vignettes/SomatiCA.Rnw