minimiseSCE {splatter} | R Documentation

## Minimise SCE

### Description

Reduce the size of a SingleCellExperiment object by unneeded information.

### Usage

    minimiseSCE(
      sce,
      rowData.keep = FALSE,
      colData.keep = FALSE,
      metadata.keep = FALSE,
      assays.keep = "counts",
      sparsify = c("auto", "all", "none"),
      verbose = TRUE
    )

### Arguments

`sce` | SingleCellExperiment object
`rowData.keep` | Either TRUE (keep all rowData columns), FALSE (remove all rowData columns) or a character vector with the names of the rowData columns to keep
`colData.keep` | Either TRUE (keep all colData columns), FALSE (remove all colData columns) or a character vector with the names of the colData columns to keep
`metadata.keep` | Either TRUE (keep all metadata), FALSE (remove all metadata) or a character vector with the names of the metadata items to keep
`assays.keep` | Either TRUE (keep all assays), FALSE (remove all assays) or a character vector with the names of the assays to keep
`sparsify` | Whether to convert assay matrices to sparse format. Either "all", "none" or "auto" (default) to only convert those matrices that will result in a size reduction
`verbose` | Whether to print status messages

### Value

SingleCellExperiment object

### Examples

    sce <- splatSimulate(verbose = FALSE)
    sce.min <- minimiseSCE(sce, verbose = FALSE)
    object.size(sce)
    object.size(sce.min)

[Package splatter version 1.18.2 Index]