run_group_hmms

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_group_hmms function

<dl><dt>bulks</dt>
<dd>dataframe Pseudobulk profiles</dd>
<dt>t</dt>
<dd>numeric Transition probability</dd>
<dt>gamma</dt>
<dd>numeric Dispersion parameter for the Beta-Binomial allele model</dd>
<dt>alpha</dt>
<dd>numeric P value cut-off to determine segment clusters in find_diploid</dd>
<dt>common_diploid</dt>
<dd>logical Whether to find common diploid regions between pseudobulks</dd>
<dt>diploid_chroms</dt>
<dd>character vector Known diploid chromosomes to use as baseline</dd>
<dt>allele_only</dt>
<dd>logical Whether only use allele data to run HMM</dd>
<dt>retest</dt>
<dd>logcial Whether to retest CNVs</dd>
<dt>run_hmm</dt>
<dd>logical Whether to run HMM segments or just retest</dd>
<dt>ncores</dt>
<dd>integer Number of cores</dd></dl>

Arguments

Run multiple HMMs — run_group_hmms

<dl>

<dt>bulks</dt>
<dd>dataframe Pseudobulk profiles</dd>


<dt>t</dt>
<dd>numeric Transition probability</dd>


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


<dt>alpha</dt>
<dd>numeric P value cut-off to determine segment clusters in find_diploid</dd>


<dt>common_diploid</dt>
<dd>logical Whether to find common diploid regions between pseudobulks</dd>


<dt>diploid_chroms</dt>
<dd>character vector Known diploid chromosomes to use as baseline</dd>


<dt>allele_only</dt>
<dd>logical Whether only use allele data to run HMM</dd>


<dt>retest</dt>
<dd>logcial Whether to retest CNVs</dd>


<dt>run_hmm</dt>
<dd>logical Whether to run HMM segments or just retest</dd>


<dt>ncores</dt>
<dd>integer Number of cores</dd>

</dl>

Run multiple HMMs

run_group_hmms: Run multiple HMMs

Description

Usage

Arguments