calc_allele_LLR

internal

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

calc_allele_LLR function

<dl><dt>pAD</dt>
<dd>numeric vector Phased allele depth</dd>
<dt>DP</dt>
<dd>numeric vector Total allele depth</dd>
<dt>R</dt>
<dd>numeric vector Allelic bias direction</dd>
<dt>p_s</dt>
<dd>numeric vector Phase switch probabilities</dd>
<dt>theta_mle</dt>
<dd>numeric MLE of imbalance level theta (alternative hypothesis)</dd>
<dt>theta_0</dt>
<dd>numeric Imbalance level in the null hypothesis</dd>
<dt>gamma</dt>
<dd>numeric Dispersion parameter for the Beta-Binomial allele model</dd></dl>

Arguments

Calculate LLR for an allele HMM — calc_allele_LLR

<dl>

<dt>pAD</dt>
<dd>numeric vector Phased allele depth</dd>


<dt>DP</dt>
<dd>numeric vector Total allele depth</dd>


<dt>R</dt>
<dd>numeric vector Allelic bias direction</dd>


<dt>p_s</dt>
<dd>numeric vector Phase switch probabilities</dd>


<dt>theta_mle</dt>
<dd>numeric MLE of imbalance level theta (alternative hypothesis)</dd>


<dt>theta_0</dt>
<dd>numeric Imbalance level in the null hypothesis</dd>


<dt>gamma</dt>
<dd>numeric Dispersion parameter for the Beta-Binomial allele model</dd>

</dl>

calc_allele_LLR: Calculate LLR for an allele HMM

Description

Usage

Value

Arguments