run_allele_hmm

internal

A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.

Teng Gao

numbat

Haplotype-Aware CNV Analysis from scRNA-Seq

Ruslan Soldatov

Hirak Sarkar

Evan Biederstedt

Peter Kharchenko

run_allele_hmm 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 copy number states</dd>
<dt>theta_min</dt>
<dd>numeric Minimum haplotype frequency deviation threshold</dd>
<dt>gamma</dt>
<dd>numeric Overdispersion in the allele-specific expression</dd></dl>

Arguments

allele-only HMM — run_allele_hmm

<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 copy number states</dd>


<dt>theta_min</dt>
<dd>numeric Minimum haplotype frequency deviation threshold</dd>


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

</dl>

allele-only HMM

run_allele_hmm: allele-only HMM

Description

Usage

Value

Arguments