index_tabular {MungeSumstats} | R Documentation |
Convert summary stats file to tabix format
index_tabular( path, chrom_col = "CHR", start_col = "BP", end_col = start_col, verbose = TRUE )
path |
Path to GWAS summary statistics file. |
chrom_col |
column for chromosome |
start_col |
column for start position |
end_col |
column for end position (is the same as start for snps) |
verbose |
Print messages. |
Path to tabix-indexed tabular file
Borrowed function from echotabix.
eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt", package = "MungeSumstats") sumstats_dt <- data.table::fread(eduAttainOkbayPth, nThread = 1) sumstats_dt <- MungeSumstats:::standardise_sumstats_column_headers_crossplatform( sumstats_dt = sumstats_dt)$sumstats_dt sumstats_dt <- MungeSumstats:::sort_coords(sumstats_dt = sumstats_dt) path <- tempfile(fileext = ".tsv") MungeSumstats::write_sumstats(sumstats_dt = sumstats_dt, save_path = path) indexed_file <- MungeSumstats::index_tabular(path = path)