BuildAUCRank: Build AUCell Rank

In huayc09/SeuratExtend: SeuratExtend

Build AUCell Rank

Description

Build AUCell ranking matrix using 'AUCell' package:

Aibar et al. (2017) SCENIC: single-cell regulatory network inference and clustering. Nature Methods. doi: 10.1038/nmeth.4463

Aibar. et al. (2016) AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data. R/Bioconductor package.

Usage

BuildAUCRank(seu, slot = "counts", assay = "RNA", verbose = TRUE)

Arguments

seu	Seurat object
slot	Slot to pull feature data for, Default: 'counts'
assay	Name of assay to use, Default: 'RNA'
verbose	Should the function show progress messages? Default: TRUE

Details

AUCell ranking matrix is saved in seu@misc$AUCell[["cells_rankings"]]

Value

Seurat object.

Examples

library(SeuratExtend)
options(max.print = 20)

pbmc <- BuildAUCRank(pbmc)
pbmc@misc$AUCell[["cells_rankings"]][3,4]

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.