CellCycleScoring_UCell: CellCycleScoring_UCell

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

CellCycleScoring_UCell

Description

Similar to Seurat's CellCycleScoring, except using UCell AddModuleScore_UCell instead of Seurat's AddModuleScore

Usage

CellCycleScoring_UCell(
  seuratObj,
  outputFieldName = "Phase",
  min.genes = 10,
  s.genes = GetSPhaseGenes(),
  g2m.genes = GetG2MGenes(TRUE),
  assayName = "RNA",
  min.score.G2M = 0.02,
  min.score.S = 0.02,
  facetField = "ClusterNames_0.2",
  ncores = 1
)

Arguments

seuratObj	The seurat object
outputFieldName	The name of the meta.data field to store results
min.genes	If less than min.genes are shared between the seurat object and the reference cell cycle genes, this method will abort.
s.genes	A vector of features associated with S phase
g2m.genes	A vector of features associated with G2M phase
assayName	The name of the assay
min.score.G2M	The minimum UCell score needed to consider a cell positive for G2M
min.score.S	The minimum UCell score needed to consider a cell positive for S
facetField	If not NA, a plot will be produced summarizing S.Core and G2M.Score, faceted by this value.
ncores	Passed directly to AddModuleScore_UCell

Value

A modified Seurat object.

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.