calculate_conditional_celltype_enrichment_limma: Calculate celltype enrichments without MAGMA

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

Calculate celltype enrichments without MAGMA

Description

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

Usage

calculate_conditional_celltype_enrichment_limma(
  magma1,
  magma2,
  ctd,
  ctd_species = infer_ctd_species(ctd),
  annotLevel = 1,
  prepare_ctd = TRUE,
  thresh = 1e-04,
  show_plot = TRUE,
  verbose = TRUE,
  ...
)

Arguments

magma1	Output from adjust_zstat_in_genesOut (e.g. trait 1).
magma2	Output from adjust_zstat_in_genesOut (e.g. trait 2).
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).
show_plot	Show plot visualizations of results (Default: TRUE).
verbose	Print messages.
...	Additional arguments passed to standardise_ctd.

Value

Data.frame with conditional enrichment results.

Examples

ctd <- ewceData::ctd()

#### MAGMA 1 #####
genesOut1 <- MAGMA.Celltyping::import_magma_files(
    ids = c("ieu-a-298"),
    file_types = ".genes.out",
    return_dir = FALSE)
magma1 <- MAGMA.Celltyping::adjust_zstat_in_genesOut(
    ctd = ctd, 
    magma_GenesOut_file = genesOut1)

#### MAGMA 2 #####
genesOut2 <- MAGMA.Celltyping::import_magma_files(
    ids = c("ukb-a-333"),
    file_types = ".genes.out",
    return_dir = FALSE)
magma2 <- MAGMA.Celltyping::adjust_zstat_in_genesOut(
    ctd = ctd, 
    magma_GenesOut_file = genesOut2)

#### Run conditional enrichment ####
cond_res <- 
MAGMA.Celltyping::calculate_conditional_celltype_enrichment_limma(
    magma1 = magma1,
    magma2 = magma2,
    ctd = ctd)

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