Extract metadata

Extract metadata as a data.frame, data.table or tibble from a list of chromatograms.

Usage

extract_metadata(
  chrom_list,
  what = chrom_metadata_fields(),
  detector = NULL,
  format_out = c("data.frame", "data.table", "tibble"),
  collapse = FALSE,
  expand = FALSE
)

Arguments

chrom_list

A list of chromatograms with attached metadata (as returned by read_chroms with read_metadata = TRUE), or a single chromatogram. Nested lists are flattened, one row per chromatogram.

what

A character vector specifying the metadata elements to extract. Defaults to every field chromConverter attaches; no format records all of them, so the elements a format does not provide are absent from the result. Superseded names (e.g. injection_volume, software_name, time_start) are accepted and mapped to the names that replaced them. An element of a nested field (see expand) may be named too, either by the column it is reported under (SampleLabel) or in full (acaml_metadata.SampleLabel), to report it without the rest of its field. A field requested by name that no chromatogram carries produces a warning.

detector

A character vector of detectors to include (e.g. "UV" or c("UV", "MS")), matched case-insensitively against each chromatogram's detector attribute. Defaults to NULL, in which case all chromatograms are included. Useful for lists containing more than one detector per sample. It is an error if no chromatogram matches.

format_out

Format of object. Either data.frame, data.table or tibble.

collapse

Logical. Whether to collapse a field holding more than one value (time_range, or the product_mz of an MRM event monitoring several transitions) into a single comma-separated string. Defaults to FALSE, in which case such a field is spread across numbered columns (time_range1, time_range2).

expand

Whether to include the nested metadata fields, whose value is itself a list or table rather than a single value per chromatogram: the ms_params instrument settings, the acaml_metadata injection record that read_agilent_rslt reads from the .acaml file, or the whole vendor list that metadata_format = "raw" passes through. Either TRUE, to include every nested field the chromatograms carry, a character vector naming the ones to include, or FALSE (the default) to include none. Each element becomes a column of its own, named for itself (SampleName) unless that name is already taken, in which case it carries the field it came from (ms_params.polarity, since polarity is a metadata field in its own right).

Value

A data.frame, tibble, or data.table (according to the value of format_out), with one row per chromatogram and the specified metadata elements as columns, or NA if none of the specified elements could be found. For a list, the first column, name, identifies each chromatogram by its path through the list (e.g. blue.UV).

Examples

path <- system.file("extdata/ladder.txt", package = "chromConverter")
chroms <- read_chroms(path, format_in = "shimadzu_ascii",
                      find_files = FALSE, progress_bar = FALSE)
extract_metadata(chroms, what = c("sample_name", "instrument", "run_datetime"))
#>     name sample_name instrument        run_datetime
#> 1 ladder    FS19_214    GC-2014 2019-07-18 19:45:56