Gather enrichment results

Gather enrichment results from celltype_associations_pipeline and converted them into harmonised, machine-readable tables.

Usage

merge_results(
  MAGMA_results,
  level = 1,
  dataset_name = NULL,
  species = "mouse",
  filetype = "ctAssocMerged",
  q_thresh = NULL,
  method = "fdr",
  save_dir = tempdir(),
  verbose = TRUE
)

Arguments

MAGMA_results

The output of celltype_associations_pipeline.

level

Which level in the CellTypeDataset (CTD) to show results for.

dataset_name

[Optional] Name of the CellTypeDataset (CTD).

species

Species that the CellTypeDataset (CTD) came from.

filetype

Type of analysis to gather the results of. These correspond to the modes of data analysis in celltype_associations_pipeline:

• "ctAssocsLinear" : Linear mode results.

• "ctAssocsTop" : Top 10% mode results.

• "ctAssocMerged" : Merged linear and top 10% results.

• "ctCondAssocs" : Conditional results.

Note: Only those analyses that were actually run in celltype_associations_pipeline can be retrieved.

q_thresh

Multiple-testing corrected p-value (q-value) filtering threshold.

method

correction method, a character string. Can be abbreviated.

save_dir

Directory to save the gathered results to.

verbose

Print messages.

Examples

if (FALSE) { # \dontrun{
#### Use precomputed results: see ?enrichment_results for details  ####
MAGMA_results <- MAGMA.Celltyping::enrichment_results

#### Merge results ####
merged_res <- MAGMA.Celltyping::merge_results(MAGMA_results)
} # }