minimiseSCE: Minimise SCE

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

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)

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.