aggregate_counts

Utility function to make reference gene expression profiles

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

aggregate_counts function

<dl><dt>count_mat</dt>
<dd>matrix/dgCMatrix Gene expression counts</dd>
<dt>annot</dt>
<dd>dataframe Cell annotation with columns "cell" and "group"</dd>
<dt>normalized</dt>
<dd>logical Whether to return normalized expression values</dd>
<dt>verbose</dt>
<dd>logical Verbosity</dd></dl>

Arguments

Utility function to make reference gene expression profiles — aggregate_counts

<dl>

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


<dt>annot</dt>
<dd>dataframe Cell annotation with columns "cell" and "group"</dd>


<dt>normalized</dt>
<dd>logical Whether to return normalized expression values</dd>


<dt>verbose</dt>
<dd>logical Verbosity</dd>

</dl>

aggregate_counts: Utility function to make reference gene expression profiles

Description

Usage

Value

Arguments

Examples