get_trans_probs_s15

Helper function to calculate transition porbabilities for 15-state joint HMM
cn/phase are sclars, only p_s is vectorized

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_trans_probs_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>cn_from</dt>
<dd>character; originating CNV state</dd>
<dt>phase_from</dt>
<dd>character; originating haplotype phase state</dd>
<dt>cn_to</dt>
<dd>character; destination CNV state</dd>
<dt>phase_to</dt>
<dd>character; destination haplotype phase state</dd></dl>

Arguments

Helper function to calculate transition porbabilities for 15-state joint HMM
cn/phase are sclars, only p_s is vectorized — get_trans_probs_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>cn_from</dt>
<dd>character; originating CNV state</dd>


<dt>phase_from</dt>
<dd>character; originating haplotype phase state</dd>


<dt>cn_to</dt>
<dd>character; destination CNV state</dd>


<dt>phase_to</dt>
<dd>character; destination haplotype phase state</dd>

</dl>

get_trans_probs_s15: Helper function to calculate transition porbabilities for 15-state joint HMM cn/phase are sclars, only p_s is vectorized

Description

Usage

Value

Arguments