Run bgzip

Compress a file using bgzip.

Usage

run_bgzip(
  target_path,
  chrom_col,
  start_col,
  end_col = start_col,
  comment_char = NULL,
  bgz_file = construct_tabix_path(target_path = target_path),
  sort_rows = TRUE,
  force_new = TRUE,
  method = c("rsamtools", "conda"),
  conda_env = "echoR_mini",
  validate = TRUE,
  verbose = TRUE
)

Arguments

target_path

Path to full GWAS/QTL summary statistics file.

chrom_col

Name of the chromosome column in the target_path file.

start_col

Name of the genomic start position column in the target_path file.

end_col

Name of the genomic end position column in the target_path file.

comment_char

A single character which, when present as the first character in a line, indicates that the line is to be omitted from indexing.

bgz_file

Path to resulting bgz-compressed file after target_path has been converted to tabix format.

sort_rows

Sort rows by genomic coordinates.

force_new

Force the creation of a new bgzip file (.bgz) and a new tabix index file (.tbi).

method

Method used to bgzip-compress the target_path file.

conda_env

Conda environments to search in. If NULL (default), will search all conda environments.

validate

Check that the bgzip file exists and can be read in as a data.table.

verbose

Print messages.

See also

Other tabix functions: construct_tabix_path(), construct_vcf_path(), convert(), index, query_table(), query_vcf(), read_bgz()

Examples

if (FALSE) { # \dontrun{
#### Example with full data ####
# tmp <- echodata::example_fullSS()
#### Example with single locus ####
dat <- echodata::BST1
tmp <- tempfile()
data.table::fwrite(dat, tmp)

bgz_file <-  echotabix::run_bgzip(target_path=tmp,
                                 chrom_col="CHR",
                                 start_col="BP")
} # }