Get MAGMA Paths — get_magma_paths • MAGMA.Celltyping

Gets paths to folders based on location of the GWAS summary statistics file. This avoids the GWAS sumstats folder becoming a mess.

get_magma_paths(
  gwas_sumstats_path = NA,
  upstream_kb = NA,
  downstream_kb = NA,
  output_path = NA
)

Source

gwas_sumstats_path <- MAGMA.Celltyping::get_example_gwas( trait = "educational_attainment") magmaPaths <- MAGMA.Celltyping:::get_magma_paths( gwas_sumstats_path = gwas_sumstats_path, upstream_kb = 35, downstream_kb = 10)

Arguments

gwas_sumstats_path: Path to the GWAS summary statistics file.
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?
output_path: If being called from magma_tileplot then gwas_sumstats_path cannot be specified, so instead specificity the base folder where MAGMA_Figures exists.

Value

File path for where MAGMA files should be created