paramSweep: paramSweep

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

paramSweep

Description

Performs pN-pK parameter sweeps on a 10,000-cell subset of a pre-processed Seurat object. Will use all cells if Seurat object contains less than 10,000 cells. Results are fed into 'summarizeSweep' and 'find.pK' functions during optimal pK parameter selection workflow. Parameters tested: pN = 0.05-0.3, pK = 0.0005-0.3.

Usage

sweep.list <- paramSweep(seu, PCs, sct=FALSE)

Arguments

seu	A fully-processed Seurat object (i.e., After NormalizeData, FindVariableGenes, ScaleData, RunPCA, and RunTSNE have all been performed).
PCs	Number of statistically-significant principal components (e.g., as estimated from PC elbow plot)
sct	Logical representing whether SCTransform was used during original Seurat object pre-processing (default = FALSE).
num.cores	Number of cores to use for parallelization, default=1.

Value

List of pANN vectors for every pN and pK combination. Output also contains pANN information for artificial doublets.

Examples

sweep.list <- paramSweep(seu, PCs = 1:10, sct=FALSE)
sweep.stats <- summarizeSweep(sweep.list, GT = FALSE)
bcmvn <- find.pK(sweep.stats)

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