get_gtree

Specify either max_cost or n_cut. 
max_cost works similarly as h and n_cut works similarly as k in stats::cutree.
The top-level normal diploid clone is always included.

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

get_gtree function

<dl><dt>tree</dt>
<dd>phylo Single-cell phylogenetic tree</dd>
<dt>P</dt>
<dd>matrix Genotype probability matrix</dd>
<dt>n_cut</dt>
<dd>integer Number of cuts on the phylogeny to define subclones</dd>
<dt>max_cost</dt>
<dd>numeric Likelihood threshold to collapse internal branches</dd></dl>

Arguments

Get a tidygraph tree with simplified mutational history. — get_gtree

<dl>

<dt>tree</dt>
<dd>phylo Single-cell phylogenetic tree</dd>


<dt>P</dt>
<dd>matrix Genotype probability matrix</dd>


<dt>n_cut</dt>
<dd>integer Number of cuts on the phylogeny to define subclones</dd>


<dt>max_cost</dt>
<dd>numeric Likelihood threshold to collapse internal branches</dd>

</dl>

get_gtree: Get a tidygraph tree with simplified mutational history.

Description

Usage

Value

Arguments