basisTest: Data-driven basis selection

In JSB-UCLA/scPNMF: scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

Data-driven basis selection

Description

Perform data-driven basis selection to remove useless bases and keep informative bases. It contains two approaches: (1) examine bases by correlations with cell library sizes; (2) examine bases by multimodality tests.

Usage

basisTest(S, X, return_fig = FALSE, adj_method = "BH", mc.cores = 10, ncol = 4)

Arguments

S	The score matrix of scPNMF.
X	The expression matrix of scPNMF.
return_fig	If returning the visualization plots. Default is FALSE.
adj_method	Multiple test correction method.
mc.cores	The number of cores to use.
ncol	Columns for facets in plots.

Author(s)

Dongyuan Song

JSB-UCLA/scPNMF documentation built on July 19, 2023, 10:28 p.m.