scoreStem: Calculate stem index

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Calculate stem index

Description

Calculate stem index at single-cell resolution using CCAT, StemSC or CytoTrace algorithms.

Usage

scoreStem(
  object,
  method = c("CCAT", "StemSC", "CytoTRACE"),
  min.pct = 0,
  assay = DefaultAssay(object),
  batch = NULL,
  verbose = T
)

Arguments

object	Seurat object
method	method used to calculate stem index. One of "CCAT", "StemSC", or "CytoTrace"
min.pct	minimum expressing fraction. Values of 0.005-0.01 recommended if data set is large.
assay	assay used for computing stem index. DefaultAssay(object) is taken if not specified.
batch	meta data feature containing batch memberships. Only used for CytoTrace algorithm.
verbose	print progress. Default is T.

Value

numeric vector

Author(s)

Nicholas Mikolajewicz

See Also

CompCCAT for computing CCAT scores, StemSC for StemSC scores, and CytoTRACE for CytoTrace scores.

Examples

ccat.score <- scoreSTEM(object = seurat.object, method = "CCAT")

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.