calc_cell_cycle: Calculate cell-cycle assignments

In hesselberthlab/scrunchy: Single Cell Reconstruction of Functional Heterogeneity

Description

Uses scran::cyclone() to assign cell-cycle phases to each cell. Assignments are available in colData in the cell_cycle slot.

Usage

calc_cell_cycle(fsce, expt = "rnaseq", org = "human", ...)

Arguments

fsce	FunctionalSingleCellExperiment
expt	Data to use for calculating variable features (default is rnaseq). Must be present in names(fsce).
org	organism for gene pairs, human or mouse
...	additional params for scran::cyclone()

References

Scialdone A, Natarajana KN, Saraiva LR et al. (2015). Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 85:54–61

Examples

fsce_small <- calc_cell_cycle(fsce_small)
SingleCellExperiment::colData(fsce_small[["rnaseq"]])

hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.