modelHomotypic: modelHomotypic

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

modelHomotypic

Description

Leverages user-provided cell annotations to model the proportion of homotypic doublets. Building on the assumption that literature-supported annotations reflect real transcriptional divergence, homotypic doublet proportions are modeled as the sum of squared annotation frequencies.

Usage

modelHomotypic(annotations)

Arguments

annotations

An nCell-length character vector of annotations.

Value

Numeric proportion of homotypic doublets.

Examples

## Initial run, nExp set to Poisson loading estimate (e.g., 913 total doublet predictions)
nExp_poi <- round(0.15*length([e-mail]))
seu <- doubletFinder(seu, pN = 0.25, pK = 0.01, nExp = nExp_poi, reuse.pANN = FALSE)

## With homotypic adjustment
homotypic.prop <- modelHomotypic(annotations)
nExp_poi.adj <- round(nExp_poi*(1-homotypic.prop))
seu <- doubletFinder(seu, pN = 0.25, pK = 0.01, nExp = nExp_poi.adj, reuse.pANN = "pANN_0.25_0.01_913")

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