parallel_paramSweep: parallel_paramSweep

In chris-mcginnis-ucsf/DoubletFinder: DoubletFinder is a suite of tools for identifying doublets in single-cell RNA sequencing data.

parallel_paramSweep

Description

Internal parallelization function for paramSweep.

Usage

**NOT RUN**
parallel_paramSweep(n, n.real.cells, real.cells, pK, pN, data, orig.commands, PCs, sct)

Arguments

n	pN iteration counter.
n.real.cells	Number of real cells. Set automatically during paramSweep_v3.
real.cells	Vector of real cell IDs. Set automatically during paramSweep_v3.
pK	The PC neighborhood size used to compute pANN, expressed as a proportion of the merged real-artificial data. No default is set, as pK should be adjusted for each scRNA-seq dataset. Optimal pK values can be determined using mean-variance-normalized bimodality coefficient.
pN	The number of generated artificial doublets, expressed as a proportion of the merged real-artificial data. Default is set to 0.25, based on observation that DoubletFinder performance is largely pN-invariant (see McGinnis, Murrow and Gartner 2019, Cell Systems).
data	Count matrix. Set automatically during paramSweep_v3.
orig.commands	Count matrix. Set automatically during paramSweep_v3.
PCs	Number of statistically-sigificant PCs. Set according to paramSweep_v3 arguments.
sct	Logical representing whether Seurat object was pre-processed using 'sctransform'. Set according to paramSweep_v3 arguments (default = F).

Value

Parallelization function compatible with mclapply.

Author(s)

Implemented by Nathan Skeene, June 2019.

chris-mcginnis-ucsf/DoubletFinder documentation built on April 12, 2024, 5:44 p.m.