MadSeq: The MadSeq class

In ykong2/MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Description

An S4 class contains estimated result returned from runMadSeq function

Slots

posterior

A matrix contains the posterior distribution from the selected model

deltaBIC

A numeric vector contains the deltaBIC value between selected model and other models. The deltaBIC between models indicate the confidence level that selected model against other models: deltaBIC ~ [0,2]: Not worth more than a bare mention deltaBIC ~ [2,6]: Positive deltaBIC ~ [6,10]: Strong deltaBIC >10: Very Strong

Accessors

In the code below, x is a MadSeq object.

posterior(x): Get the matrix containing posterior distribution of selected model.

deltaBIC(x): Get the deltaBIC between selected model and other models

Summary

In the code below, x is a MadSeq object.

summary(x): summarize the posterior distribution

MadSeq Methods

In the code below, x is a MadSeq object.

plotMadSeq(x): Plot the posterior distribution of all parameters in selected model.

plotFraction(x): Plot the estimated distribution of the fraction of aneuploid sample.

plotMixture(x): Plot the distribution of AAF estimated from the selected model.

Author(s)

Yu Kong

See Also

runMadSeq, plotMadSeq

ykong2/MADSEQ documentation built on May 4, 2019, 5:30 p.m.