celltype_associations_pipeline: Calculate cell type associations using MAGMA

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

Calculate cell type associations using MAGMA

Description

Has the option of running multiple analyses with a single function. Assumes that you already have all MAGMA GWAS files precomputed. Precomputed MAGMA GWAS files can be downloaded via the import_magma_files function.

Usage

celltype_associations_pipeline(
  ctd,
  ctd_levels = seq_len(length(ctd)),
  ctd_name,
  ctd_species = infer_ctd_species(ctd),
  standardise = TRUE,
  magma_dirs,
  run_linear = TRUE,
  run_top10 = TRUE,
  run_conditional = FALSE,
  upstream_kb = 35,
  downstream_kb = 10,
  suffix_linear = "linear",
  suffix_top10 = "top10",
  suffix_condition = "condition",
  controlledAnnotLevel = 1,
  controlTopNcells = 1,
  force_new = FALSE,
  save_dir = tempdir(),
  nThread = 1,
  version = NULL,
  verbose = TRUE
)

Arguments

ctd	Cell type data structure containing specificity_quantiles.
ctd_levels	Which levels of ctd to iterate the enrichment analysis over.
ctd_name	Used in file names
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.
standardise	Whether to run standardise_ctd first. Provides gene ortholog conversion.
magma_dirs	Path to folders containing the pre-computed MAGMA GWAS files (.gsa.rawand .gsa.out). NOTE: Files within these folders must have the same naming scheme as the folders themselves.
run_linear	Run in linear mode.
run_top10	Run in top 10% mode.
run_conditional	Run in conditional mode.
upstream_kb	How many kb upstream of the gene should SNPs be included?
downstream_kb	How many kb downstream of the gene should SNPs be included?
suffix_linear	This will be added to the linear results file name.
suffix_top10	This will be added to the top 10% results file name.
suffix_condition	This will be added to the conditional results file name.
controlledAnnotLevel	Which annotation level should be controlled for.
controlTopNcells	How many of the most significant cell types at that annotation level should be controlled for?
force_new	[Optional] Force new MAGMA analyses even if the pre-existing results files are detected.
save_dir	Folder to save results in (save_dir=NULL to not save any results).
nThread	Number of threads to parallelise analyses across.
version	MAGMA version to use.
verbose	Print messages.

Value

A list containing the results of each selected celltype associations analysis.

Examples

magma_dirs <- MAGMA.Celltyping::import_magma_files(ids = c("ieu-a-298"))
ctd <- ewceData::ctd()

res <- MAGMA.Celltyping::celltype_associations_pipeline(
    ctd = ctd,
    ctd_levels = 1,
    ctd_name = "Zeisel2015",
    ctd_species = "mouse",
    magma_dirs = magma_dirs)

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