calculate_geneset_enrichment: Use MAGMA to test enrichment in a geneset

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

Use MAGMA to test enrichment in a geneset

Description

Assumes that you have already run map_snps_to_genes.

Usage

calculate_geneset_enrichment(
  geneset,
  gwas_sumstats_path = NULL,
  magma_dir = NULL,
  analysis_name,
  upstream_kb = 35,
  downstream_kb = 10,
  geneset_species = "mouse",
  version = NULL,
  verbose = TRUE
)

Arguments

geneset	Genes which are to be tested. Can be gene symbols (or other gene IDs) from any species listed in list_species.
gwas_sumstats_path	File path of the summary statistics file.
magma_dir	Path to folder containing the pre-computed MAGMA GWAS files (.gsa.rawand .gsa.out).
analysis_name	Used in file names which area created.
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?
geneset_species	Species that the geneset came from. Can be any species listed in list_species. If geneset_species!="human", the geneset will be converted to 1:1 human orthologs using convert_orthologs.
version	MAGMA version to use.
verbose	Print messages.

Value

Filepath for the genes.out file.

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