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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", "benzoxazinoid_standards",
                    package = "chromConverter")
chroms <- read_chroms(path, format_in = "chemstation_ch", pattern = "dad1A",
                      parser = "chromconverter", progress_bar = FALSE)
subset(chroms, sample_name != "MEOH")
#> A chrom_list with 9 chromatograms
#> method: ETHAN_DT_MEOH_L16-6.M  |  detector: DAD  |  wavelength: 254
#>              name     sample_name        run_datetime
#> 1  BENZOS_1000PPM  benzos_1000ppm 2023-06-20 19:29:41
#> 2   BENZOS_500PPM   benzos_500ppm 2023-06-21 15:23:43
#> 3   BENZOS_250PPM   benzos_250ppm 2023-06-21 16:46:40
#> 4   BENZOS_125PPM   benzos_125ppm 2023-06-21 18:02:48
#> 5  BENZOS_62,5PPM  benzos_62,5ppm 2023-06-21 19:19:00
#> 6 BENZOS_31,25PPM benzos_31,25ppm 2023-06-21 20:35:12
#> 7    BENZOS_16PPM    benzos_16ppm 2023-06-21 21:51:21
#> 8     BENZOS_8PPM     benzos_8ppm 2023-06-21 23:07:28
#> 9     BENZOS_4PPM     benzos_4ppm 2023-06-22 00:23:39
subset(chroms, run_datetime < as.POSIXct("2023-06-21", tz = "UTC"))
#> A chrom_list with 2 chromatograms
#> method: ETHAN_DT_MEOH_L16-6.M  |  detector: DAD  |  wavelength: 254
#>             name    sample_name        run_datetime
#> 1           MEOH           MEOH 2023-06-15 16:46:23
#> 2 BENZOS_1000PPM benzos_1000ppm 2023-06-20 19:29:41