Merge multiple CellTypeDataset references

Import CellTypeDataset (CTD) references from a remote repository, standardize each, and then merge into one CTD. Optionally, can return these as a merged SingleCellExperiment.

merge_ctd(
  CTD_list,
  save_dir = tempdir(),
  standardise_CTD = FALSE,
  as_SCE = FALSE,
  gene_union = TRUE,
  merge_levels = seq(1, 5),
  save_split_SCE = FALSE,
  save_split_CTD = FALSE,
  save_merged_SCE = TRUE,
  force_new_quantiles = FALSE,
  numberOfBins = 40,
  as_sparse = TRUE,
  as_DelayedArray = FALSE,
  verbose = TRUE,
  ...
)

Arguments

CTD_list: (Named) list of CellTypeDatasets.
save_dir: The directory to save merged files in.
standardise_CTD: Whether to run standardise_ctd.
as_SCE: If TRUE (default), returns the merged results as a named list of SingleCellExperiments. If FALSE, returns as a CTD object.
gene_union: Whether to take the gene union or intersection when merging matrices (mean_exp,specificity, etc.).
merge_levels: Which CTD levels you want to merge. Can be a single value (e.g. merge_levels=5) or a list c(e.g. merge_levels=c(1:5)). If some CTD don't have the same number of levels, the maximum level depth available in that CTD will be used instead.
save_split_SCE: Whether to save individual SCE files in the subdirectory standardized_CTD_SCE.
save_split_CTD: Whether to save individual CTD files in the subdirectory standardized_CTD.
save_merged_SCE: Save the final merged SCE object, or simply to return it.
force_new_quantiles: If specificity quantiles matrix already exists, create a new one.
numberOfBins: Number of bins to compute specificity quantiles with.
as_sparse: Convert matrices to sparse matrix.
as_DelayedArray: Convert matrices to DelayedArray.
verbose: Print messages.
...: Additional arguments to be passed to standardise_ctd.

Value

List of CellTypeDatasets or SingleCellExperiments.

Examples

## Let's pretend these are different CTD datasets
ctd1 <- ewceData::ctd()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
ctd2 <- ctd1
CTD_list <- list(ctd1, ctd2)
CTD_merged <- EWCE::merge_ctd(CTD_list = CTD_list)
#> + Must set `as_SCE=TRUE` in order to merge CTD.
#> + Returning merged CTD.
#> 1 core(s) assigned as workers (3 reserved).
#> Converting to sparse matrix.
#> + Calculating normalized mean expression.
#> Converting to sparse matrix.
#> + Calculating normalized specificity.
#> Converting to sparse matrix.
#> Converting to sparse matrix.
#> + Saving results ==>  /tmp/RtmpuXbkZF/ctd_file39857076e01blevel_1.rda
#> + Returning list of CTD file name, and the CTD itself.
#> 1 core(s) assigned as workers (3 reserved).
#> Converting to sparse matrix.
#> + Calculating normalized mean expression.
#> Converting to sparse matrix.
#> + Calculating normalized specificity.
#> Converting to sparse matrix.
#> Converting to sparse matrix.
#> + Saving results ==>  /tmp/RtmpuXbkZF/ctd_file39855c21b68elevel_2.rda
#> + Returning list of CTD file name, and the CTD itself.