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.

Author(s)

Chris McGinnis

Examples

## Initial run, nExp set to Poisson loading estimate (e.g., 913 total
## doublet predictions)
data(pbmc_small)
seu <- pbmc_small
nExp_poi <- round(0.15*length(seu$RNA_snn_res.1))
seu <- doubletFinder(seu,
                     PCs = 1:10,
                     pN = 0.25,
                     pK = 0.01,
                     nExp = nExp_poi,
                     reuse.pANN = FALSE)

## With homotypic adjustment
annotations <- [e-mail]$RNA_snn_res.1
homotypic.prop <- modelHomotypic(annotations)
nExp_poi.adj <- round(nExp_poi*(1-homotypic.prop))
seu <- doubletFinder(seu, pN = 0.25,
                     PCs = 1:10,
                     pK = 0.01,
                     nExp = nExp_poi.adj,
                     reuse.pANN = FALSE)

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