genotype

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

genotype function

<dl><dt>label</dt>
<dd>character Individual/sample label</dd>
<dt>samples</dt>
<dd>vector Sample names</dd>
<dt>vcfs</dt>
<dd>list of vcfR VCFs from cellsnp-lite pileup</dd>
<dt>outdir</dt>
<dd>character Output directory</dd>
<dt>het_only</dt>
<dd>logical Whether to only use heterozygous SNPs</dd>
<dt>chr_prefix</dt>
<dd>logical Whether to add chr prefix</dd></dl>

Arguments

Genotyping main function — genotype

<dl>

<dt>label</dt>
<dd>character Individual/sample label</dd>


<dt>samples</dt>
<dd>vector Sample names</dd>


<dt>vcfs</dt>
<dd>list of vcfR VCFs from cellsnp-lite pileup</dd>


<dt>outdir</dt>
<dd>character Output directory</dd>


<dt>het_only</dt>
<dd>logical Whether to only use heterozygous SNPs</dd>


<dt>chr_prefix</dt>
<dd>logical Whether to add chr prefix</dd>

</dl>

Genotyping main function

genotype: Genotyping main function

Description

Usage

Value

Arguments