Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Documentation for package ‘MADSEQ’ version 1.4.1

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