merge_ctd: Merge multiple CellTypeDataset references

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Merge multiple CellTypeDataset references

Description

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

Usage

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()
ctd2 <- ctd1
CTD_list <- list(ctd1, ctd2)
CTD_merged <- EWCE::merge_ctd(CTD_list = CTD_list)

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.