Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data


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Documentation for package ‘MADSEQ’ version 1.31.0

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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