hahmmr1.0.0 package

Analyze allele profile

Analyze allele and expression profile

Annotate genetic distance between markers

Annotate copy number segments after HMM decoding

Laplace approximation of the posterior of expression fold change phi

Find optimal theta of a CNV segment using forward-backward; uses a 2-s...

Find optimal theta of a chromosome using forward-backward; uses a 3-st...

Calculate allele likelihoods for 2-state allele HMM

Calculate allele likelihoods for 3-state allele HMM

Calculate LLR for an allele HMM

Calculate LLR for an expression HMM

Calculate the transition matrix for 15-state joint HMM

Calculate the transition matrix for 7-state joint HMM

Check if columns are present in dataframe

Check the format of a count matrix

classify alleles using viterbi and forward-backward

Combine allele and expression pseudobulks

Beta-binomial distribution density function A distribution is beta-bin...

Returns the density for the Poisson lognormal distribution with parame...

filter for mutually expressed genes

fit gamma maximum likelihood

Fit MLE of log-normal Poisson model

Fit a reference profile from multiple references using constrained lea...

Forward-backward algorithm for allele HMM

Generate alphabetical postfixes

Aggregate into pseudobulk alelle profile

Make a 2-state allele HMM - no transitions to netural state

Make a 3-state allele HMM - allow transitions to netural state

Produce combined bulk expression and allele profile

Aggregate into bulk expression profile

Helper function to calculate transition porbabilities for 15-state joi...

Helper function to calculate transition porbabilities for 7-state join...

calculate joint likelihood of allele data

calculate joint likelihood of a PLN model

Only compute total log likelihood from an allele HMM

logSumExp function

Plot a group of pseudobulk HMM profiles

Plot a pseudobulk HMM profile

Run a 3-state allele HMM

Run a 5-state allele-only HMM - two theta levels

Run 15-state joint HMM on a pseudobulk profile

Run 7-state joint HMM on a pseudobulk profile

Smooth the segments after HMM decoding

predict phase switch probablity as a function of genetic distance

Estimate of imbalance level theta in a segment

Viterbi algorithm for allele HMM

Viterbi algorithm for joint HMM, can only handle one set of observatio...

Generalized viterbi algorithm for joint HMM, can handle multiple sets ...