create_fake_gwas_path: Create a fake GWAS path when all you have are the MAGMA files

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

Create a fake GWAS path when all you have are the MAGMA files

Description

Necessary to trick calculate_celltype_associations and calculate_conditional_celltype_associations to take MAGMA files (".genes.raw" and ".genes.out") alone.

Usage

create_fake_gwas_path(
  magma_dir,
  upstream_kb = 35,
  downstream_kb = 10,
  remove_pattern = "/MAGMA_Files/"
)

Arguments

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?

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