index_tabular {MungeSumstats}R Documentation

Convert summary stats file to tabix format

Description

Convert summary stats file to tabix format

Usage

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

Arguments

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.

Value

Path to tabix-indexed tabular file

Source

Borrowed function from echotabix.

Examples

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)

[Package MungeSumstats version 1.2.1 Index]