load_scGate_model

Loads a custom scGate model into R. For the format of these models, have a
look or edit one of the default models obtained with <code>get_scGateDB</code>

A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of sparsity in scRNA-seq data. Finally, a universal threshold over kNN-smoothed signature scores is applied in binary decision trees generated from the user-provided gating model, to annotate cells as either “pure” or “impure”, with respect to the cell population of interest. See the related publication Andreatta et al. (2022) <doi:10.1093/bioinformatics/btac141>.

Massimo Andreatta

scGate

Marker-Based Cell Type Purification for Single-Cell Sequencing
Data

Ariel Berenstein

Josep Garnica

Santiago Carmona

load_scGate_model function

<dl><dt>model_file</dt>
<dd>scGate model file, in .tsv format.</dd>
<dt>master.table</dt>
<dd>File name of the master table (in repo_path folder) that contains cell type signatures.</dd></dl>

Arguments

Load a single scGate model — load_scGate_model

<dl>

<dt>model_file</dt>
<dd>scGate model file, in .tsv format.</dd>


<dt>master.table</dt>
<dd>File name of the master table (in repo_path folder) that contains cell type signatures.</dd>

</dl>

load_scGate_model: Load a single scGate model

Description

Usage

Value

Arguments

See Also

Examples