SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
Version 2.2.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorMengjie Chen <mengjie.chen@yale.edu>, Hongyu Zhao <hongyu.zhao@yale.edu>
Date of publicationNone
MaintainerMengjie Chen <mengjie.chen@yale.edu>
LicenseGPL (>=2)
Version2.2.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SomatiCA")

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...

Functions

GCbiasRemoval Man page
GCcontent Man page
GCcount Man page
MergeSegment Man page
SomatiCA Man page
SomatiCA-package Man page
SomatiCAFormat Man page
SomatiCAFormat,GRanges-method Man page
SomatiCAFormat,character-method Man page
SomatiCAFormat,data.frame-method Man page
SomatiCAFormat-methods Man page
SomatiCAUsersGuide Man page
SomatiCApipe Man page
admixtureRate Man page
collapse Man page
copynumberCorrected Man page
denoise Man page
larsCBSsegment Man page
plotSegment Man page
plotSubclonality Man page
refineSegment Man page
segmentGCbiasRemoval Man page
segwithratio Man page
somaticRatio Man page
subclonality Man page

Files

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
SomatiCA documentation built on Oct. 5, 2016, 4:18 a.m.