Write sum stats file to disk

Write sum stats file to disk

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

Source

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

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.

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.

Examples

path <- system.file("extdata", "eduAttainOkbay.txt",
    package = "MungeSumstats"
)
eduAttainOkbay <- read_sumstats(path = path)
#> Importing tabular file: /__w/_temp/Library/MungeSumstats/extdata/eduAttainOkbay.txt
#> Checking for empty columns.
write_sumstats(
    sumstats_dt = eduAttainOkbay,
    save_path = tempfile(fileext = ".tsv.gz")
)
#> Writing in tabular format ==> /tmp/RtmpmswcRa/file1480205a5222.tsv.gz