get_example_gwas: Import GWAS summary statistics

View source: R/get_example_gwas.R

get_example_gwasR Documentation

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.