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 |