preprocess_allele

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

preprocess_allele function

<dl><dt>sample</dt>
<dd>character Sample label</dd>
<dt>vcf_pu</dt>
<dd>dataframe Pileup VCF from cell-snp-lite</dd>
<dt>vcf_phased</dt>
<dd>dataframe Phased VCF from eagle2</dd>
<dt>AD</dt>
<dd>dgTMatrix Alt allele depth matrix from pileup</dd>
<dt>DP</dt>
<dd>dgTMatrix Total allele depth matrix from pileup</dd>
<dt>barcodes</dt>
<dd>vector List of barcodes from pileup</dd>
<dt>gtf</dt>
<dd>dataframe Transcript GTF</dd>
<dt>gmap</dt>
<dd>dataframe Genetic map</dd></dl>

Arguments

Preprocess allele data — preprocess_allele

<dl>

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


<dt>vcf_pu</dt>
<dd>dataframe Pileup VCF from cell-snp-lite</dd>


<dt>vcf_phased</dt>
<dd>dataframe Phased VCF from eagle2</dd>


<dt>AD</dt>
<dd>dgTMatrix Alt allele depth matrix from pileup</dd>


<dt>DP</dt>
<dd>dgTMatrix Total allele depth matrix from pileup</dd>


<dt>barcodes</dt>
<dd>vector List of barcodes from pileup</dd>


<dt>gtf</dt>
<dd>dataframe Transcript GTF</dd>


<dt>gmap</dt>
<dd>dataframe Genetic map</dd>

</dl>

Preprocess allele data

preprocess_allele: Preprocess allele data

Description

Usage

Value

Arguments