run_bgzip: Run bgzip

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

Run bgzip

Description

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

#### 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")

RajLabMSSM/echotabix documentation built on Nov. 21, 2023, 8:02 a.m.