rliger (version 2.0.1)

retrieveCellFeature: Retrieve a single matrix of cells from a slot

Description

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,
  ...
)

Value

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

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".

Examples

S100A8Exp <- retrieveCellFeature(pbmc, "S100A8")
qcMetrics <- retrieveCellFeature(pbmc, c("nUMI", "nGene", "mito"),
                                 slot = "cellMeta")