likelihood_allele

Only compute total log likelihood from an allele HMM

Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Additional examples, documentations, and details on the method are available at <https://github.com/kharchenkolab/hahmmr/>.

Teng Gao

hahmmr

Haplotype-Aware Hidden Markov Model for RNA

Evan Biederstedt

Peter Kharchenko

likelihood_allele function

<dl><dt>hmm</dt>
<dd>HMM object; expect variables x (allele depth), d (total depth),
logPi (log transition prob matrix), delta (prior for each state),
alpha (alpha for each state), beta (beta for each state),
states (states), p_s (phase switch probs)</dd></dl>

Arguments

Only compute total log likelihood from an allele HMM — likelihood_allele

<dl>

<dt>hmm</dt>
<dd>HMM object; expect variables x (allele depth), d (total depth),
logPi (log transition prob matrix), delta (prior for each state),
alpha (alpha for each state), beta (beta for each state),
states (states), p_s (phase switch probs)</dd>

</dl>

likelihood_allele: Only compute total log likelihood from an allele HMM

Description

Usage

Value

Arguments

Examples