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]