get_example_gwas: Import GWAS summary statistics

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

Import GWAS summary statistics

Description

Write example GWAS summary statistics to disk. All examples originally come from the UK Biobank. To reduce file size, SNPs have been filtered to Minor Allele Frequency (MAF) > 5 recommend using full GWAS summary statistics (after applying format_sumstats).

Usage

get_example_gwas(
  trait = c("educational_attainment", "fluid_intelligence", "prospective_memory"),
  munged = TRUE,
  storage_dir = tools::R_user_dir("MAGMA.Celltyping", which = "cache"),
  timeout = 60 * 5,
  verbose = TRUE
)

Arguments

trait	Which trait to get GWAS summary stats for.
munged	Whether to download the raw or pre-munged version of each GWAS (Default: TRUE).
storage_dir	Folder in which to store the GWAS summary stats.
timeout	How many seconds to wait before timeout.
verbose	Print messages.

Value

Path to downloaded GWAS summary statistics.

Source

#### fluid_intelligence #### gwas_sumstats_path <- MAGMA.Celltyping::get_example_gwas( trait = "fluid_intelligence", munged = FALSE) path_formatted <- MungeSumstats::format_sumstats( path=gwas_sumstats_path, save_path = tempfile(fileext = ".formatted.tsv.gz"), ref_genome ="GRCh37") ss <- data.table::fread(path_formatted) ss2 <- ss[MINOR_AF>=.05 & P<.05,] data.table::fwrite(ss2, path_formatted, sep = "\t") piggyback::pb_upload(file = path_formatted, name = "fluid_intelligence.ukb.tsv.gz", repo = "neurogenomics/MAGMA_Celltyping", overwrite = TRUE) #### prospective_memory #### gwas_sumstats_path <- MAGMA.Celltyping::get_example_gwas( trait = "prospective_memory", munged = FALSE) path_formatted <- MungeSumstats::format_sumstats( path=gwas_sumstats_path, save_path = tempfile(fileext = ".formatted.tsv.gz"), ref_genome ="GRCh37") ss <- data.table::fread(path_formatted) ss2 <- ss[MINOR_AF>=.05 & P<.05,] data.table::fwrite(ss2, path_formatted, sep = "\t") piggyback::pb_upload(file = path_formatted, name = "prospective_memory.ukb.tsv.gz", repo = "neurogenomics/MAGMA_Celltyping", overwrite = TRUE)

Examples

path_formatted <- MAGMA.Celltyping::get_example_gwas()

NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.