Generate the results table — orbi_summarize

Contains the logic to generate the results table. It passes the ratio_method parameter to the orbi_calculate_summarized_ratio() function for ratio calculations.

Usage

orbi_summarize_results(
  dataset,
  ratio_method = c("mean", "sum", "median", "geometric_mean", "slope", "weighted_sum"),
  .by = c("block", "sample_name", "segment", "data_group", "data_type", "injection"),
  include_flagged_data = FALSE,
  include_unused_data = FALSE
)

Arguments

dataset

A tibble from IsoX output (orbi_read_isox()) and with a basepeak already defined (using orbi_define_basepeak()). Optionally, with block definitions (orbi_define_blocks_for_dual_inlet()) or even additional block segments (orbi_segment_blocks()).

ratio_method

Method for computing the ratio. Please note well: the formula used to calculate ion ratios matters! Do not simply use arithmetic mean. The best option may depend on the type of data you are processing (e.g., MS1 versus M+1 fragmentation). ratio_method can be one of the following:

mean: arithmetic mean of ratios from individual scans.
sum: sum of all ions of the numerator across all scans divided by the sum of all ions observed for the denominator across all scans.
geometric_mean: geometric mean of ratios from individual scans.
slope: The ratio is calculated using the slope obtained from a linear regression model that is weighted by the numerator x, using stats::lm(x ~ y + 0, weights = x).
weighted_sum: A derivative of the sum option. The weighing function ensures that each scan contributes equal weight to the ratio calculation, i.e. scans with more ions in the Orbitrap do not contribute disproportionately to the total sum of x and y that is used to calculate x/y.

.by

additional grouping columns for the results summary (akin to dplyr's .by parameter e.g. in dplyr::summarize()). If not set by the user, all columns in the parameter's default values are used, if present in the dataset. Note that the order of these is also used to arrange the summary.

include_flagged_data

whether to include flagged data in the calculations (FALSE by default)

include_unused_data

whether to include unused data in the calculations (FALSE by default), in addition to peaks actually flagged as setting("data_type_data")

Value

Returns a results summary table retaining the columns filename, compound, isotopocule and basepeak as well as the grouping columns from the .by parameter that are part of the input dataset. Additionally this function adds the following results columns: start_scan.no, end_scan.no, start_time.min, mean_time.min, end_time.min, ratio, ratio_sem, ratio_relative_sem_permil, shot_noise_permil, No.of.Scans, minutes_to_1e6_ions

ratio: The isotope ratio between the isotopocule and the basepeak, calculated using the ratio_method
ratio_sem: Standard error of the mean for the ratio
number_of_scans: Number of scans used for the final ratio calculation
minutes_to_1e6_ions: Time in minutes it would take to observe 1 million ions of the isotopocule used as numerator of the ratio calculation.
shot_noise_permil: Estimate of the shot noise (more correctly thermal noise) of the reported ratio in permil.
ratio_relative_sem_permil: Relative standard error of the reported ratio in permil

Examples

fpath <- system.file("extdata", "testfile_flow.isox", package = "isoorbi")
df <- orbi_read_isox(file = fpath) |>
      orbi_simplify_isox() |>
      orbi_define_basepeak("M0")  |>
      orbi_summarize_results(ratio_method = "sum")
#> orbi_read_isox() is loading .isox data from 1 file(s)...
#> - loaded 6449 peaks for 1 compounds (HSO4-) with 5 isotopocules (M0, 33S,
#>    17O, 34S, 18O) from testfile_flow.isox in 0.02 seconds.
#> orbi_simplify_isox() will keep only columns 'filepath', 'filename',
#>    'scan.no', 'time.min', 'compound', 'isotopocule', 'ions.incremental',
#>    'tic', 'it.ms'...
#>    ...complete in 0.00 seconds.
#> orbi_define_basepeak() is setting the 'M0' isotopocule as the ratio
#>    denominator...
#>    ...set base peak and calculated 5159 ratios for 4 isotopocules/base peak
#>    (33S, 17O, 34S, 18O) in 0.06 seconds.
#> orbi_summarize_results() is grouping the data by 'filename', 'compound',
#>    'basepeak', 'isotopocule' and summarizing ratios from 5159 peaks (excluded
#>    0 flagged peaks; excluded 0 unused peaks) using the 'sum' method...
#>    ...completed in 0.02 seconds.