selectFeatures {celda} | R Documentation

## Simple feature selection by feature counts

### Description

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`.

### Usage

    selectFeatures(x, ...)

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

    ## S4 method for signature '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.
`...` | Ignored. Placeholder to prevent check warning.
`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)

[Package celda version 1.6.1 Index]