write_sumstats {MungeSumstats}R Documentation

Write sum stats file to disk

Description

Write sum stats file to disk

Usage

write_sumstats(
  sumstats_dt,
  save_path,
  sep = "\t",
  write_vcf = FALSE,
  tabix_index = FALSE,
  nThread = 1,
  return_path = 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").

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).

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).

Value

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

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")
)
[Package MungeSumstats version 1.2.4 Index]