minimiseSCE {splatter} | R Documentation |
Reduce the size of a SingleCellExperiment object by unneeded information.
minimiseSCE( sce, rowData.keep = FALSE, colData.keep = FALSE, metadata.keep = FALSE, assays.keep = "counts", sparsify = c("auto", "all", "none"), verbose = TRUE )
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 |
SingleCellExperiment object
sce <- splatSimulate(verbose = FALSE) sce.min <- minimiseSCE(sce, verbose = FALSE) object.size(sce) object.size(sce.min)