Simple feature selection by feature counts

Source: R/selectFeatures.R

A simple heuristic feature selection procedure. Select features with at least minCount counts in at least minCell cells. A SingleCellExperiment object with subset features will be stored in the altExp slot with name altExpName. The name of the assay slot in altExp will be the same as useAssay.

selectFeatures(
  x,
  minCount = 3,
  minCell = 3,
  useAssay = "counts",
  altExpName = "featureSubset"
)

# S4 method for SingleCellExperiment
selectFeatures(
  x,
  minCount = 3,
  minCell = 3,
  useAssay = "counts",
  altExpName = "featureSubset"
)

# S4 method for matrix
selectFeatures(
  x,
  minCount = 3,
  minCell = 3,
  useAssay = "counts",
  altExpName = "featureSubset"
)

Arguments

x

A numeric matrix of counts or a SingleCellExperiment with the matrix located in the assay slot under useAssay. Rows represent features and columns represent cells.

minCount

Minimum number of counts required for feature selection.

minCell

Minimum number of cells required for feature selection.

useAssay

A string specifying the name of the assay slot to use. Default "counts".

altExpName

The name for the altExp slot to use. Default "featureSubset".

Value

A SingleCellExperiment object with a

altExpName

altExp slot. Function parameter settings are stored in the metadata

"select_features" slot.

Examples

data(sceCeldaCG)
sce <- selectFeatures(sceCeldaCG)
data(celdaCGSim)
sce <- selectFeatures(celdaCGSim$counts)