retrieveCellFeature: Retrieve a single matrix of cells from a slot

In rliger: Linked Inference of Genomic Experimental Relationships

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,
  ...
)

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

rliger documentation built on Oct. 30, 2024, 1:07 a.m.