Read bgz

Read a compressed bgz file into R.

Usage

read_bgz(
  path,
  method = c("data.table", "utils"),
  nrows = NULL,
  header = TRUE,
  verbose = TRUE,
  ...
)

Arguments

path

Path to bgz-compressed file.

method

Method to use to import bgz file.

nrows

The maximum number of rows to read. Unlike read.table, you do not need to set this to an estimate of the number of rows in the file for better speed because that is already automatically determined by fread almost instantly using the large sample of lines. nrows=0 returns the column names and typed empty columns determined by the large sample; useful for a dry run of a large file or to quickly check format consistency of a set of files before starting to read any of them.

header

Does the first data line contain column names? Defaults according to whether every non-empty field on the first data line is type character. If so, or TRUE is supplied, any empty column names are given a default name.

verbose

Be chatty and report timings?

...

Additional arguments passed to fread or read.delim2.

Details

NOTE: Packages like Rsamtools and seqminer aren't great for this because they require that the bgz file it also indexed already.

See also

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

Examples

if (FALSE) { # \dontrun{
tmp <- tempfile(fileext = ".tsv.gz")
data.table::fwrite(echodata::BST1, file = tmp, sep = "\t")
path <- Rsamtools::bgzip(file = tmp, overwrite=TRUE)
dat <- echotabix::read_bgz(path=path, method="utils")
} # }