robustSingleCell (version 0.1.1)

cell.cycle.score: Compute Cell Cycle Score

Description

Compute the activation of cell cycle genes defined in Kowalczyk, M. S. et al.

Usage

cell.cycle.score(environment, knn = 10, cc.genes.path = NA)

Arguments

environment

environment object

knn

number of nearest neighbor

cc.genes.path

optional; path to defined cell cycle genes. Default uses gene sets defined in Kowalczyk, M. S. et al. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Res 25, 1860-1872, doi:10.1101/gr.192237.115 (2015).

Value

a matrix of cell cycle genes activation scores (S, G2M and aggregated S/G2M scores, separately)

Examples

# NOT RUN {
LCMV1 <- setup_LCMV_example()
cell.cycle.score <- cell.cycle.score(LCMV1)
# }