Tabix-index file: table

Source: R/index_tabular.R

Convert summary stats file to tabix format.

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

Source

Borrowed function from echotabix.

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

See also

Other tabix: index_vcf()

Examples

sumstats_dt <- MungeSumstats::formatted_example() 
#> Standardising column headers.
#> First line of summary statistics file: 
#> MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
#> Sorting coordinates.
path <- tempfile(fileext = ".tsv")
MungeSumstats::write_sumstats(sumstats_dt = sumstats_dt, save_path = path)
#> Writing in tabular format ==> /tmp/RtmpmswcRa/file14806ae6bb9c.tsv
indexed_file <- MungeSumstats::index_tabular(path = path)
#> Converting full summary stats file to tabix format for fast querying...
#> Reading header.
#> Ensuring file is bgzipped.
#> Tabix-indexing file.
#> Removing temproary .tsv file.