detect_clonal_loh

Call clonal LOH using SNP density. 
Rcommended for cell lines or tumor samples with no normal cells.

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

detect_clonal_loh function

<dl><dt>bulk</dt>
<dd>dataframe Pseudobulk profile</dd>
<dt>t</dt>
<dd>numeric Transition probability</dd>
<dt>snp_rate_loh</dt>
<dd>numeric The assumed SNP density in clonal LOH regions</dd>
<dt>min_depth</dt>
<dd>integer Minimum coverage to filter SNPs</dd></dl>

Arguments

Call clonal LOH using SNP density. 
Rcommended for cell lines or tumor samples with no normal cells. — detect_clonal_loh

<dl>

<dt>bulk</dt>
<dd>dataframe Pseudobulk profile</dd>


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


<dt>snp_rate_loh</dt>
<dd>numeric The assumed SNP density in clonal LOH regions</dd>


<dt>min_depth</dt>
<dd>integer Minimum coverage to filter SNPs</dd>

</dl>

detect_clonal_loh: Call clonal LOH using SNP density. Rcommended for cell lines or tumor samples with no normal cells.

Description

Usage

Value

Arguments

Examples