calc_trans_mat_s15

Calculate the transition matrix for 15-state joint HMM

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_trans_mat_s15 function

<dl><dt>t</dt>
<dd>numeric; CNV state transition probability</dd>
<dt>p_s</dt>
<dd>numeric; phase switch probability</dd>
<dt>w</dt>
<dd>numeric; relative abundance of states</dd>
<dt>states_cn</dt>
<dd>character; CNV states</dd>
<dt>states_phase</dt>
<dd>character; haplotype phase states</dd></dl>

Arguments

Calculate the transition matrix for 15-state joint HMM — calc_trans_mat_s15

<dl>

<dt>t</dt>
<dd>numeric; CNV state transition probability</dd>


<dt>p_s</dt>
<dd>numeric; phase switch probability</dd>


<dt>w</dt>
<dd>numeric; relative abundance of states</dd>


<dt>states_cn</dt>
<dd>character; CNV states</dd>


<dt>states_phase</dt>
<dd>character; haplotype phase states</dd>

</dl>

calc_trans_mat_s15: Calculate the transition matrix for 15-state joint HMM

Description

Usage

Value

Arguments