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
Examples
sce <- splatSimulate(verbose = FALSE)
sce.min <- minimiseSCE(sce, verbose = FALSE)
object.size(sce)
#> 46071400 bytes
object.size(sce.min)
#> 5509392 bytes