find.pK: find.pK

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

find.pK

Description

Computes and visualizes the mean-variance normalized bimodality coefficient (BCmvn) score for each pK value tested during doubletFinder_ParamSweep. Optimal pK for any scRNA-seq data can be manually discerned as maxima in BCmvn distributions. If ground-truth doublet classifications are available, BCmvn is plotted along with mean ROC AUC for each pK.

Usage

find.pK(sweep.stats)

Arguments

sweep.stats

pN-pK bimodality coefficient dataframe as produced by summarizeSweep.

Value

Dataframe of mean BC, BC variance, and BCmvn scores for each pK value. Includes mean AUC for each pK value if ground-truth doublet classifications are utilized during summarizeSweep.

Author(s)

Chris McGinnis

Examples

data(pbmc_small)
seu <- pbmc_small
sweep.list <- paramSweep(seu)
sweep.stats <- summarizeSweep(sweep.list, GT = FALSE)
bcmvn <- find.pK(sweep.stats)

chris-mcginnis-ucsf/DoubletFinder documentation built on Feb. 4, 2025, 7:44 p.m.