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Select chromatograms by their metadata

Source: R/chrom_list-methods.R
subset.chrom_list.Rd

Retains the chromatograms of a chrom_list whose metadata meet the specified condition, such as sample_name == "blank" or run_datetime > as.POSIXct("2024-01-01", tz = "UTC"). The condition can refer to any field extract_metadata reports, such as sample_name or method, as well as the chromatogram's name in the list.

Usage

# S3 method for class 'chrom_list'
subset(x, subset, ...)

Arguments

x

A chrom_list object.

subset

An expression giving a single TRUE or FALSE for each chromatogram.

...

Ignored.

Value

A chrom_list containing the selected chromatograms.

Details

Numeric fields such as time_range and sample_injection_volume compare as numbers wherever the file's value parses as one, and a field with several values can be indexed (e.g. time_range[2]). A field a chromatogram does not carry is NA, and a chromatogram for which subset is NA is dropped, as in subset() for data frames. Where an element holds several chromatograms, such as the traces read_agilent_d returns for each .D directory, it is kept or dropped as a whole, and subset sees the fields its chromatograms agree on, ignoring those that leave a field empty; a field they disagree on is NA.

See also

extract_metadata

Examples

path <- system.file("extdata/ladder.txt", package = "chromConverter")
chroms <- read_chroms(path, format_in = "shimadzu_ascii",
                      find_files = FALSE, progress_bar = FALSE)
subset(chroms, sample_name == "FS19_214")
#> A chrom_list with 1 chromatogram
#> name: ladder  |  sample_name: FS19_214  |  run_datetime: 2019-07-18 19:45:56
#>   method: C:\LabSolutions\Data\A Legan\Method files\SPME_sample_1.gcm
subset(chroms, grepl("ladder", source_file))
#> A chrom_list with 1 chromatogram
#> name: ladder  |  sample_name: FS19_214  |  run_datetime: 2019-07-18 19:45:56
#>   method: C:\LabSolutions\Data\A Legan\Method files\SPME_sample_1.gcm