calculate_celltype_enrichment_limma: Calculate celltype enrichment

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

Calculate celltype enrichment

Description

Calculate celltype enrichments without MAGMA using adjusted MAGMA Z-statistic from .genes.out files.

Usage

calculate_celltype_enrichment_limma(
  magmaAdjZ,
  ctd,
  ctd_species = infer_ctd_species(ctd = ctd),
  annotLevel = 1,
  prepare_ctd = TRUE,
  thresh = 1e-04,
  celltypes = NULL,
  return_all = FALSE,
  verbose = TRUE,
  ...
)

Arguments

magmaAdjZ	Output from adjust_zstat_in_genesOut.
ctd	Cell type data structure containing specificity_quantiles.
ctd_species	Species name relevant to the CellTypeDataset (ctd). See list_species for all available species. If ctd_species=NULL (default), the ctd species will automatically be inferred using infer_species.
annotLevel	Level within the ctd to use.
prepare_ctd	Whether to run prepare_quantile_groups on the ctd first.
thresh	A threshold on low specificity values (used to drop genes).
celltypes	Cell types to conduct tests for. Defaults to all cell types available in selected ctd level.
return_all	Return a list of both the processed data input and the enrichment results (Default). If FALSE, will only return enrichment results.
verbose	Print messages.
...	Additional arguments passed to standardise_ctd.

Examples

ctd <- ewceData::ctd()

# The package stores an example genesOut file, so save this to a tempfile
myGenesOut <- MAGMA.Celltyping::import_magma_files(
    ids = c("ieu-a-298"),
    file_types = ".genes.out",
    return_dir = FALSE)
    
#### Get adjust gene z-scores ####    
magmaAdjZ <- MAGMA.Celltyping::adjust_zstat_in_genesOut(
    ctd = ctd,
    magma_GenesOut_file = myGenesOut)
    
#### Get cell type enrichment ####
ps <- MAGMA.Celltyping::calculate_celltype_enrichment_limma(
    magmaAdjZ = magmaAdjZ,
    ctd = ctd)

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