compute_MAGMA_enrichment_discrete: Compute MAGMA enrichment

In alexandruioanvoda/gwascelltyper: Fast GWAS Enrichment Testing

Compute MAGMA enrichment

Description

Compute GWAS enrichment in discrete lists of genes with MAGMA.

Usage

compute_MAGMA_enrichment_discrete(
  gene_sets,
  genesets_conditioned_for = NULL,
  sumstats_file,
  output_dir = NULL,
  upstream_kb = 10,
  downstream_kb = 1.5,
  gene_nomenclature = "hgnc",
  pop = "eur",
  gwas_sample_size = NULL,
  deps = dep_path(pop, "magma")
)

Arguments

gene_sets	List of genesets. Each geneset must be a character vector, containing HGNC gene names.
genesets_conditioned_for	Character vector of name(s) of the geneset(s) (from the above list) that should be conditioned for (if NULL, no geneset is conditioned for). Default is NULL.
sumstats_file	Address of properly formatted MAGMA GWAS file.
output_dir	Folder where you want the output to be stored. Default = NULL, which makes this function create a directory where results will be temporarily stored. The directory will be deleted afterwards, if this parameter is null. The only output will be the return. Otherwise, both the files and the return are kept.
upstream_kb	Number of kb upstream of gene, SNP-to-gene mapping window. Default = 10.
downstream_kb	Number of kb downstream of gene, SNP-to-gene mapping window. Default = 1.5.
gene_nomenclature	Type of gene IDs fed in from the expression data (default = hgnc; alternatives = entrez).
pop	Word describing ancestry of the GWAS data. Relevant so that the proper LD panel will be used (default = eur; alternatives = afr, amr, eas, sas, subpop)
gwas_sample_size	Sample size of GWAS.
deps	A named list, containing all of the dependencies for MAGMA (e.g. executables, SNP linkage disequilibrium data, etc.). Provided by default by another function, called gwascelltyper::dep_path().

Value

Dataframe

alexandruioanvoda/gwascelltyper documentation built on April 16, 2023, 8:03 p.m.