MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Version 1.2.0

The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.

Browse man pages Browse package API and functions Browse package files

AuthorYu Kong, Adam Auton, John Murray Greally
Bioconductor views Bayesian CopyNumberVariation Coverage GenomicVariation Sequencing SomaticMutation VariantDetection
Date of publicationNone
MaintainerYu Kong <yu.kong@phd.einstein.yu.edu>
LicenseGPL(>=2)
Version1.2.0
URL https://github.com/ykong2/MADSEQ
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MADSEQ")

Man pages

aneuploidy_chr18: An S4 class MadSeq object
deltaBIC: Accessing delta BIC of MadSeq object
MadSeq: The MadSeq class
MADSEQ-package: Mosaic Aneuploidy Detection using Massive Parallel Sequencing...
normalizeCoverage: correct coverage bias due to GC content
plotFraction: histgram for the fraction of aneuploid cells estimated by...
plotMadSeq: density plot for posterior distribution of selected model
plotMixture: density plot for the posterior distribution of alternative...
posterior: Accessing posterior distribution of MadSeq object
prepareCoverageGC: get sequencing coverage and GC content for targeted regions
prepareHetero: prepare heterozygous sites for aneuploidy detection
runMadSeq: Model to detect and quantify mosaic aneuploidy
summary-method: Summarize statistics of the MadSeq object

Functions

HDIofMCMC Source code
MADSEQ-package Man page
MadSeq Man page
MadSeq-class Man page
aneuploidy_chr18 Man page
calculateGC Source code
calculateNormedCoverage Source code
calculateSubCoverage Source code
calculate_BIC Source code
correctGCBias Source code
coverageQuantile Source code
creatDataList_Four Source code
creatDataList_LOH Source code
creatDataList_One Source code
creatDataList_Two Source code
deltaBIC Man page
deltaBIC,MadSeq-method Man page
getCoverage Source code
isHetero Source code
log_likelihood_UPD Source code
log_likelihood_four Source code
log_likelihood_one Source code
log_likelihood_two Source code
normalizeCoverage Man page Source code
plotFraction Man page
plotFraction,MadSeq-method Man page
plotMadSeq Man page
plotMadSeq,MadSeq-method Man page
plotMixture Man page
plotMixture,MadSeq-method Man page
plotSites Source code
posterior Man page
posterior,MadSeq-method Man page
prepareCoverageGC Man page Source code
prepareHetero Man page Source code
runLOH Source code
runMadSeq Man page Source code
runMeioticTrisomy Source code
runMitoticTrisomy Source code
runMonosomy Source code
runNormal Source code
summary Man page
summary,MadSeq-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/MADSEQ.R
R/MadSeqMethod.R
R/PlotHelper.R
R/PlotShow.R
R/PreProcessingHelper.R
R/PreProcessingShow.R
R/RunModelHelper.R
R/RunModelShow.R
R/data.R
README.md
build
build/vignette.rds
data
data/aneuploidy_chr18.RData
inst
inst/NEWS
inst/doc
inst/doc/MADSEQ-vignette.R
inst/doc/MADSEQ-vignette.Rmd
inst/doc/MADSEQ-vignette.html
inst/extdata
inst/extdata/aneuploidy.bam
inst/extdata/aneuploidy.bam.bai
inst/extdata/aneuploidy.vcf.gz
inst/extdata/aneuploidy.vcf1.gz
inst/extdata/normal.bam
inst/extdata/normal.bam.bai
inst/extdata/normal.vcf.gz
inst/extdata/target.bed
inst/rjags
inst/rjags/FourMix.txt
inst/rjags/LOH.txt
inst/rjags/OneMix.txt
inst/rjags/TwoMixMonosomy.txt
inst/rjags/TwoMixTrisomy.txt
man
man/MADSEQ-package.Rd
man/MadSeq.Rd
man/aneuploidy_chr18.Rd
man/deltaBIC.Rd
man/normalizeCoverage.Rd
man/plotFraction.Rd
man/plotMadSeq.Rd
man/plotMixture.Rd
man/posterior.Rd
man/prepareCoverageGC.Rd
man/prepareHetero.Rd
man/runMadSeq.Rd
man/summary-method.Rd
vignettes
vignettes/MADSEQ-vignette.Rmd
MADSEQ documentation built on May 20, 2017, 10:46 p.m.