write_sumstats: Write sum stats file to disk

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Write sum stats file to disk

Description

Write sum stats file to disk

Usage

write_sumstats(
  sumstats_dt,
  save_path,
  ref_genome = NULL,
  sep = "\t",
  write_vcf = FALSE,
  save_format = NULL,
  tabix_index = FALSE,
  nThread = 1,
  return_path = FALSE,
  save_path_check = FALSE
)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS.
save_path	File path to save formatted data. Defaults to tempfile(fileext=".tsv.gz").
ref_genome	name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.
sep	The separator between columns. Defaults to the character in the set [,\t |;:] that separates the sample of rows into the most number of lines with the same number of fields. Use NULL or "" to specify no separator; i.e. each line a single character column like base::readLines does.
write_vcf	Whether to write as VCF (TRUE) or tabular file (FALSE).
save_format	Output format of sumstats. Options are NULL - standardised output format from MungeSumstats, LDSC - output format compatible with LDSC and openGWAS - output compatible with openGWAS VCFs. Default is NULL. NOTE - If LDSC format is used, the naming convention of A1 as the reference (genome build) allele and A2 as the effect allele will be reversed to match LDSC (A1 will now be the effect allele). See more info on this here. Note that any effect columns (e.g. Z) will be inrelation to A1 now instead of A2.
tabix_index	Index the formatted summary statistics with tabix for fast querying.
nThread	The number of threads to use. Experiment to see what works best for your data on your hardware.
return_path	Return save_path. This will have been modified in some cases (e.g. after compressing and tabix-indexing a previously un-compressed file).
save_path_check	Ensure path name is valid (given the other arguments) before writing (default: FALSE).

Value

If return_path=TRUE, returns save_path. Else returns NULL.

Source

VariantAnnotation::writeVcf has some unexpected/silent file renaming behavior

Examples

path <- system.file("extdata", "eduAttainOkbay.txt",
    package = "MungeSumstats"
)
eduAttainOkbay <- read_sumstats(path = path)
write_sumstats(
    sumstats_dt = eduAttainOkbay,
    save_path = tempfile(fileext = ".tsv.gz")
)

neurogenomics/MungeSumstats documentation built on May 2, 2024, 9:04 a.m.