merge_results: Gather enrichment results

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Gather enrichment results

Description

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

## Not run: 
#### Use precomputed results: see ?enrichment_results for details  ####
MAGMA_results <- MAGMA.Celltyping::enrichment_results

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

## End(Not run)

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.