Score cell cycle phases

Source: R/utilities.R

Score cell cycle phases

CellCycleScoring(
  object,
  s.features,
  g2m.features,
  ctrl = NULL,
  set.ident = FALSE,
  ...
)

Arguments

object

A Seurat object

s.features

A vector of features associated with S phase

g2m.features

A vector of features associated with G2M phase

ctrl

Number of control features selected from the same bin per analyzed feature supplied to AddModuleScore. Defaults to value equivalent to minimum number of features present in 's.features' and 'g2m.features'.

set.ident

If true, sets identity to phase assignments Stashes old identities in 'old.ident'

...

Arguments to be passed to AddModuleScore

Value

A Seurat object with the following columns added to object meta data: S.Score, G2M.Score, and Phase

See also

AddModuleScore

Examples

if (FALSE) {
data("pbmc_small")
# pbmc_small doesn't have any cell-cycle genes
# To run CellCycleScoring, please use a dataset with cell-cycle genes
# An example is available at http://satijalab.org/seurat/cell_cycle_vignette.html
pbmc_small <- CellCycleScoring(
  object = pbmc_small,
  g2m.features = cc.genes$g2m.genes,
  s.features = cc.genes$s.genes
)
head(x = pbmc_small@meta.data)
}