compute_bjk_enrichment_discrete: Complete block jackknife joint test

In alexandruioanvoda/gwascelltyper: Fast GWAS Enrichment Testing

Complete block jackknife joint test

Description

Compute GWAS enrichment in discrete lists of genes with the block jackknife joint test.

Usage

compute_bjk_enrichment_discrete(
  gene_sets,
  sumstats_files,
  output_dir,
  pop = "eur",
  n_blocks = 200,
  number_of_threads = 1
)

Arguments

gene_sets	List of genesets. Each geneset must be a character vector, containing HGNC gene names.
sumstats_files	Addresses of properly formatted MAGMA and LDSC-formatted files for GWAS summary statistics.
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.
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)
n_blocks	The number of blocks to split the genome into (default = 200).
number_of_threads	Number of threads to parallelize over.

Value

List

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