Calculate cell-cycle assignments

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

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

# \donttest{
fsce_small <- calc_cell_cycle(fsce_small)
SingleCellExperiment::colData(fsce_small[["rnaseq"]])
#> DataFrame with 250 rows and 4 columns
#>                           cell_id   k_cluster leiden_cluster  cell_cycle
#>                       <character> <character>    <character> <character>
#> TGCGGGTGTAGAGTGC TGCGGGTGTAGAGTGC           2              2           S
#> TGGTTCCCATCTATGG TGGTTCCCATCTATGG           6              4           S
#> CATATTCCACGTCAGC CATATTCCACGTCAGC           2              2         G2M
#> TCACAAGTCCTGCTTG TCACAAGTCCTGCTTG           5              3          G1
#> GGAATAATCCAGGGCT GGAATAATCCAGGGCT           4              4          G1
#> ...                           ...         ...            ...         ...
#> CTACGTCCACCACGTG CTACGTCCACCACGTG           6              4          G1
#> TGTGGTAAGGTGCTTT TGTGGTAAGGTGCTTT           3              6          G1
#> AGCGTCGGTCGAGTTT AGCGTCGGTCGAGTTT           3              6          G1
#> CTCGAAAAGTTCGATC CTCGAAAAGTTCGATC           6              5         G2M
#> TGACAACGTCGCATAT TGACAACGTCGCATAT           6              4           S
# }