make_group_bulks

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

make_group_bulks function

<dl><dt>groups</dt>
<dd>list Contains fields named "sample", "cells", "size", "members"</dd>
<dt>count_mat</dt>
<dd>dgCMatrix Gene counts</dd>
<dt>df_allele</dt>
<dd>dataframe Alelle counts</dd>
<dt>lambdas_ref</dt>
<dd>matrix Reference expression profiles</dd>
<dt>gtf</dt>
<dd>dataframe Transcript GTF</dd>
<dt>min_depth</dt>
<dd>integer Minimum allele depth to include</dd>
<dt>segs_loh</dt>
<dd>dataframe Segments with clonal LOH to be excluded</dd>
<dt>ncores</dt>
<dd>integer Number of cores</dd></dl>

Arguments

Make a group of pseudobulks — make_group_bulks

<dl>

<dt>groups</dt>
<dd>list Contains fields named "sample", "cells", "size", "members"</dd>


<dt>count_mat</dt>
<dd>dgCMatrix Gene counts</dd>


<dt>df_allele</dt>
<dd>dataframe Alelle counts</dd>


<dt>lambdas_ref</dt>
<dd>matrix Reference expression profiles</dd>


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


<dt>min_depth</dt>
<dd>integer Minimum allele depth to include</dd>


<dt>segs_loh</dt>
<dd>dataframe Segments with clonal LOH to be excluded</dd>


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

</dl>

Make a group of pseudobulks

make_group_bulks: Make a group of pseudobulks

Description

Usage

Value

Arguments