SC_cellCycleScoring: Score cell cycle phases Cell cycle classification including...

In FanqianYin/omicstoolkits: Integrated bioinformatics toolkits for quantitative omics data analysis

Description

Score cell cycle phases Cell cycle classification including G2/M, S, G1.

Usage

SC_cellCycleScoring(
  counts,
  method = "Seurat",
  graph.pca = TRUE,
  cc.genes = NULL,
  normalization.method = "LogNormalize"
)

Arguments

counts	raw counts matrix: row as genes, column as cells/samples. rownames must be gene SYMBOL.
method	one of: "Seurat",
graph.pca	whether to show pca graph which only based on 97 cell cycle genes or not.
cc.genes	a list, with cc.genes and s.genes vectors. Defult are cc.genes from Seurat package.
normalization.method	Method for counts normalization: "LogNormalize", "CLR", "RC". see NormalizeData

Value

factor vector for classfication (G1, G2/M, S)

See Also

https://satijalab.org/seurat/v3.2/cell_cycle_vignette.html

FanqianYin/omicstoolkits documentation built on Jan. 3, 2022, 5:57 p.m.