Retrieve a single matrix of cells from a slot — retrieveCellFeature • rliger

Only retrieve data from specific slot to reduce memory used by a whole liger object of the subset. Useful for plotting. Internally used by plotDimRed and plotCellViolin.

Usage

retrieveCellFeature(
  object,
  feature,
  slot = c("rawData", "normData", "scaleData", "H", "H.norm", "cellMeta", "rawPeak",
    "normPeak"),
  cellIdx = NULL,
  ...
)

Arguments

object: liger object
feature: Gene names, factor index or cell metadata variable names. Should be available in specified slot.
slot: Exactly choose from "rawData", "normData", "scaleData", "H", "H.norm" or "cellMeta".
cellIdx: Any valid type of index that subset from all cells. Default NULL uses all cells.
...: Additional arguments passed to subsetLiger when slot is one of "rawData", "normData" or "scaleData".

Value

A matrix object where rows are cells and columns are specified features.

Examples

S100A8Exp <- retrieveCellFeature(pbmc, "S100A8")
#> ℹ Subsetting dataset: "ctrl"
#> ℹ Subsetting dataset: "stim"
#> ✔ Subsetting dataset: "stim" ... done
#> 
#> ℹ Subsetting dataset: "ctrl"

#> ✔ Subsetting dataset: "ctrl" ... done
#> 
qcMetrics <- retrieveCellFeature(pbmc, c("nUMI", "nGene", "mito"),
                                 slot = "cellMeta")