Summarize a chrom_list object

Returns what print.chrom_list displays as a table, with one row per chromatogram: the sample it belongs to, its size, and the metadata fields in cols. Unlike print, nothing is collapsed into a header, abbreviated or truncated to the first few rows, so the result can be filtered and joined against.

Usage

# S3 method for class 'chrom_list'
summary(
  object,
  cols = chrom_summary_cols(),
  format_out = c("data.frame", "data.table", "tibble"),
  digits = NULL,
  ...
)

Arguments

object: A chrom_list object.
cols: Character vector of attribute names to report. Defaults to: sample_name, run_datetime, method, detector, wavelength, detector_range, scan_type, polarity, precursor_mz, product_mz, mz_range. A field that no chromatogram carries, or that all of them leave empty, is omitted rather than filled with NA.
format_out: Format of object. Either data.frame, data.table or tibble.
digits: Number of significant digits for the numbers in a field collapsed into a string, or NULL (the default) to keep them in full.
...: Additional arguments (currently ignored).

Value

A data.frame, data.table or tibble (according to the value of format_out) with one row per chromatogram. The first columns describe where the chromatogram sits and how large it is — sample, trace (only when a sample holds more than one), n_rows and n_cols — followed by one column per metadata field found. A field no chromatogram records, or that every one of them leaves empty, is dropped rather than filled with NA. A field holding more than one value, such as the product_mz of an MRM event monitoring several transitions, is collapsed to a comma-separated string so that it occupies one column.

Examples

path <- system.file("extdata", "benzoxazinoid_standards",
                    package = "chromConverter")
chroms <- read_chroms(path, format_in = "chemstation_ch", pattern = "dad1A",
                      parser = "chromconverter", progress_bar = FALSE)
summary(chroms)
#>             sample n_rows n_cols     sample_name        run_datetime
#> 1             MEOH   9000      1            MEOH 2023-06-15 16:46:23
#> 2   BENZOS_1000PPM   9001      1  benzos_1000ppm 2023-06-20 19:29:41
#> 3    BENZOS_500PPM   9001      1   benzos_500ppm 2023-06-21 15:23:43
#> 4    BENZOS_250PPM   9000      1   benzos_250ppm 2023-06-21 16:46:40
#> 5    BENZOS_125PPM   9001      1   benzos_125ppm 2023-06-21 18:02:48
#> 6   BENZOS_62,5PPM   9001      1  benzos_62,5ppm 2023-06-21 19:19:00
#> 7  BENZOS_31,25PPM   9000      1 benzos_31,25ppm 2023-06-21 20:35:12
#> 8     BENZOS_16PPM   9001      1    benzos_16ppm 2023-06-21 21:51:21
#> 9      BENZOS_8PPM   9001      1     benzos_8ppm 2023-06-21 23:07:28
#> 10     BENZOS_4PPM   9001      1     benzos_4ppm 2023-06-22 00:23:39
#>                   method detector wavelength
#> 1  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 2  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 3  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 4  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 5  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 6  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 7  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 8  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 9  ETHAN_DT_MEOH_L16-6.M      DAD        254
#> 10 ETHAN_DT_MEOH_L16-6.M      DAD        254

Usage

Arguments

Value

See also

Examples