index_tabular: Tabix-index file: table

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Tabix-index file: table

Description

Convert summary stats file to tabix format.

Usage

index_tabular(
  path,
  chrom_col = "CHR",
  start_col = "BP",
  end_col = start_col,
  overwrite = TRUE,
  remove_tmp = TRUE,
  verbose = TRUE
)

Arguments

path	Path to GWAS summary statistics file.
chrom_col	Name of the chromosome column in sumstats_dt (e.g. "CHR").
start_col	Name of the starting genomic position column in sumstats_dt (e.g. "POS","start").
end_col	Name of the ending genomic position column in sumstats_dt (e.g. "POS","end"). Can be the same as start_col when sumstats_dt only contains SNPs that span 1 base pair (bp) each.
overwrite	A logical(1) indicating whether dest should be over-written, if it already exists.
remove_tmp	Remove the temporary uncompressed version of the file (.tsv).
verbose	Print messages.

Value

Path to tabix-indexed tabular file

Source

Borrowed function from echotabix.

See Also

Other tabix: index_vcf()

Examples

sumstats_dt <- MungeSumstats::formatted_example() 
path <- tempfile(fileext = ".tsv")
MungeSumstats::write_sumstats(sumstats_dt = sumstats_dt, save_path = path)
indexed_file <- MungeSumstats::index_tabular(path = path)

neurogenomics/MungeSumstats documentation built on July 17, 2024, 3:14 p.m.