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
)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)