Merge multiple CellTypeDataset references

Import CellTypeDataset (CTD) references from a remote repository, standardize each, and then merge into one CTD.

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 =T, will return a the merged CTD as a SingleCellExperiment. Otherwise, will return a list of unmerged CTD.
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 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.

Details

Optionally, can return these as a merged SingleCellExperiment.

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)
SCE_merged <- EWCE::merge_ctd(
    CTD_list = CTD_list,
    as_SCE = TRUE,
    gene_union = TRUE
)
#> Converting CTD to merged SCEs
#> ctd1
#> + CTD ==> SingleCellExperiment
#> Converting level:  level_1
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting level:  level_2
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> ctd2
#> + CTD ==> SingleCellExperiment
#> Converting level:  level_1
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting level:  level_2
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Converting to sparse matrix.
#> Converting to DelayedArray.
#> Merging SCE at level: 1
#> [1] "ctd1"
#> [1] "15259 x 7"
#> [1] "ctd2"
#> [1] "15259 x 7"
#> The assay named 'mean_exp' will be used to determine theproportion of zeroes for each batch
#> Merging SCE at level: 2
#> [1] "ctd1"
#> [1] "15259 x 48"
#> [1] "ctd2"
#> [1] "15259 x 48"
#> The assay named 'mean_exp' will be used to determine theproportion of zeroes for each batch
#> [1] "level_1"
#> [1] "level_2"
#> Saving SCE_merged ==> /tmp/Rtmp5DLuZU/merged/CTD_SCE_merged.union.rds