get_allele_hmm_s3

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

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

get_allele_hmm_s3 function

<dl><dt>pAD</dt>
<dd>integer vector Paternal allele counts</dd>
<dt>DP</dt>
<dd>integer vector Total alelle counts</dd>
<dt>p_s</dt>
<dd>numeric vector Phase switch probabilities</dd>
<dt>t</dt>
<dd>numeric Transition probability between haplotype states</dd>
<dt>theta_min</dt>
<dd>numeric Haplotype imbalance</dd>
<dt>gamma</dt>
<dd>numeric Overdispersion in the allele-specific expression</dd>
<dt>r</dt>
<dd>numeric Variant mapping bias</dd></dl>

Arguments

Make a 3-state allele HMM - allow transitions to netural state — get_allele_hmm_s3

<dl>

<dt>pAD</dt>
<dd>integer vector Paternal allele counts</dd>


<dt>DP</dt>
<dd>integer vector Total alelle counts</dd>


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


<dt>t</dt>
<dd>numeric Transition probability between haplotype states</dd>


<dt>theta_min</dt>
<dd>numeric Haplotype imbalance</dd>


<dt>gamma</dt>
<dd>numeric Overdispersion in the allele-specific expression</dd>


<dt>r</dt>
<dd>numeric Variant mapping bias</dd>

</dl>

get_allele_hmm_s3: Make a 3-state allele HMM - allow transitions to netural state

Description

Usage

Value

Arguments