Predicting Ploidal Level from Sequence Data

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Documentation for package ‘nQuack’ version 1.0.4

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

Help Pages

alphabetacalc	Calculate Alpha and Beta from Mean and Variance
alphabetacalctau	Calculate Alpha and Beta from Mean, Tau, and Error rate.
alphabetacalctauvec	Vector-based - Calculate Alpha and Beta from Mean, Tau, and Error rate.
alphabetacalcvec	Vector-based - Calculate Alpha and Beta from Mean and Variance
Bclean	Remove Noise with the Beta Distribution
bestquack	Model Selection - Expectation Maximization - Optimal Distribution and Type
denoise_data	Denoise Data
emstepB	Expectation maximization - Beta Distribution
emstepB3	Expectation maximization - Beta + Beta + Beta Distribution
emstepBB	Expectation maximization - Beta-Binomial Distribution
emstepBBU	Expectation maximization - Beta-Binomial and Uniform Distributions
emstepBU	Expectation maximization - Beta and Uniform Distributions
emstepN	Expectation maximization - Normal Distribution
emstepNA	Expectation maximization - Normal Distribution
emstepNU	Expectation maximization - Normal and Uniform Distribution
emstepNUA	Expectation maximization - Normal Distribution
estepB3	E-Step for Expectation Maximization - Beta + Beta + Beta Distribution
muvarcalcvec	Variance calculation from Mean, Tau, and Sequencing Error
nQuire_reformat	Data Preparation - Use nQuire's Data
prepare_data	Prepare Data - Step 1
process_data	Process Data - Step 2
process_nquire	Use nQuire's Data
process_rcpp	Data Preparation - Matrix Filtering
quackBeta	Model Selection - Expectation Maximization - Beta Mixture
quackBetaBinom	Model Selection - Expectation Maximization - Beta-Binomial Mixture
quackit	Model Selection - Based on BIC or Log-Likelihood
quackNboots	Bootstrapping - Expectation Maximization - Optimal Distribution and Type
quackNormal	Model Selection - Expectation Maximization - Normal Mixture
quackNormalNQ	Model Selection - Expectation Maximization - Normal Mixture (nQuire)
resample_xm	Calculate Alpha and Beta from Mean and Variance
setconvert	Calculate Variance from Mean, Tau, and Sequencing Error
SetupBasicExample	Setup Basic Example
sim.ind.BB	Simulate Allele Counts for Single Individual - Beta-Binomial Distribution
sim.ind.BB.tau	Simulate Allele Counts for Single Individual - Beta-Binomial Distribution with Overdispersion and Error
sim.ind.simple	Simulate Allele Counts for Single Individual - Simple Approach