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Read files recursively in the ANEMONE DB data directory.

Source: R/read.R
read.Rd

ANEMONE DB contains a large collection of small tables, and this package provides efficient ways to read and process them. It may take a while to run them for the first time, but subsequent runs will be very quick because the results are cached.

Usage

read_tsv_xz(filename, compress = NULL, ..., limit = 250L, force = FALSE)

Arguments

filename

A filename to read. Files are searched recursively in the path returned by directory_prefix(). It should be one of the following:

  • community_qc3nn_target.tsv.xz

  • community_qc_target.tsv.xz

  • community_standard.tsv.xz

  • experiment.tsv.xz

  • sample.tsv.xz

compress

Compression method to use: "gz", "bz2", "xz" or "". If NULL (default), the same one as the input file is used.

...

Additional arguments passed to readr::read_tsv().

limit

Maximum number of files to read at once.

force

Set to TRUE to ignore and overwrite existing files in cache_dir().

Value

A concatenated data frame.

See also

https://db.anemone.bio/about-data/

Examples

if (FALSE) { # \dontrun{
ranemone::read_tsv_xz("sample.tsv.xz")
ranemone::read_tsv_xz("experiment.tsv.xz")
ranemone::read_tsv_xz("community_qc3nn_target.tsv.xz")
} # }