# Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

## Documentation for package ‘MADSEQ’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

MADSEQ-package | Mosaic Aneuploidy Detection using Massive Parallel Sequencing Data (MADSEQ)
aneuploidy_chr18 | An S4 class MadSeq object
deltaBIC | Accessing delta BIC of MadSeq object
deltaBIC-method | Accessing delta BIC of MadSeq object
MadSeq | The MadSeq class
MadSeq-class | The MadSeq class
normalizeCoverage | correct coverage bias due to GC content
plotFraction | histgram for the fraction of aneuploid cells estimated by MadSeq model
plotFraction-method | histgram for the fraction of aneuploid cells estimated by MadSeq model
plotMadSeq | density plot for posterior distribution of selected model
plotMadSeq-method | density plot for posterior distribution of selected model
plotMixture | density plot for the posterior distribution of alternative allele frequency estimated from the selected model
plotMixture-method | density plot for the posterior distribution of alternative allele frequency estimated from the selected model
posterior | Accessing posterior distribution of MadSeq object
posterior-method | 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 | Summarize statistics of the MadSeq object
summary-method | Summarize statistics of the MadSeq object