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

Share:

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.

Author
Yu Kong, Adam Auton, John Murray Greally
Date of publication
None
Maintainer
Yu Kong <yu.kong@phd.einstein.yu.edu>
License
GPL(>=2)
Version
1.0.0
URLs

View on Bioconductor

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

Files in this package

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