Add metadata to a list of chromatograms

Attaches the columns of a table to the chromatograms of a chrom_list as metadata fields, matching each row to a sample by name. The new fields can then be used by subset.chrom_list and requested from extract_metadata. Where an element holds several chromatograms, such as the traces read_agilent_d returns for each .D directory, every one of them gets the sample's values.

Usage

add_metadata(chrom_list, metadata, by = "name", overwrite = FALSE)

Arguments

chrom_list

A chrom_list object.

metadata

A data.frame, tibble or data.table with one row per sample.

by

The column of metadata holding the sample names, matched to names(chrom_list). Defaults to name, the column extract_metadata identifies samples by.

overwrite

Whether a column may replace a field that chromConverter reads from the file, such as sample_name. Defaults to FALSE, in which case such a column is an error.

Value

chrom_list with the columns of metadata attached to its chromatograms, and their names recorded in an added_metadata attribute, from which chromatographR's get_peaktable fills its sample_meta. A sample without a row in metadata is left unchanged, with a warning.

See also

extract_metadata, subset.chrom_list

Examples

path <- system.file("extdata", "benzoxazinoid_standards",
                    package = "chromConverter")
chroms <- read_chroms(path, format_in = "chemstation_ch", pattern = "dad1A",
                      parser = "chromconverter", progress_bar = FALSE)
meta <- data.frame(name = c("MEOH", "BENZOS_1000PPM", "BENZOS_500PPM",
                            "BENZOS_250PPM", "BENZOS_125PPM",
                            "BENZOS_62,5PPM", "BENZOS_31,25PPM",
                            "BENZOS_16PPM", "BENZOS_8PPM", "BENZOS_4PPM"),
                   ppm = c(0, 1000 / 2^(0:8)))
chroms <- add_metadata(chroms, meta)
extract_metadata(chroms, what = "ppm")
#>               name        ppm
#> 1             MEOH    0.00000
#> 2   BENZOS_1000PPM 1000.00000
#> 3    BENZOS_500PPM  500.00000
#> 4    BENZOS_250PPM  250.00000
#> 5    BENZOS_125PPM  125.00000
#> 6   BENZOS_62,5PPM   62.50000
#> 7  BENZOS_31,25PPM   31.25000
#> 8     BENZOS_16PPM   15.62500
#> 9      BENZOS_8PPM    7.81250
#> 10     BENZOS_4PPM    3.90625
names(subset(chroms, ppm >= 250))
#> [1] "BENZOS_1000PPM" "BENZOS_500PPM"  "BENZOS_250PPM"