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Filter peak lists

Source: R/filter_peaks.R
filter_peaks.Rd

Filters peaks from a peak_list object by height, area, width, retention time, or fit diagnostics (converged and window_limited).

Usage

filter_peaks(
  peak_list,
  min_height,
  min_area,
  min_sd,
  max_sd,
  min_rt,
  max_rt,
  min_fwhm,
  max_fwhm,
  converged,
  window_limited
)

Arguments

peak_list

A peak_list object, consisting of a nested list of peak tables, where the first level is the sample, and the second level is the spectral wavelength. Every sample × wavelength component is described by a data.frame where every row represents a peak, and the columns contain information on retention time, peak shape, height, and area.

min_height

Minimum peak height. Peaks whose height is NA, such as failed fits kept by get_peaks, are dropped if min_height is supplied and retained otherwise.

min_area

Minimum peak area. Peaks whose area is NA are treated the same way.

min_sd

The min_sd argument is deprecated. Please use min_fwhm instead.

max_sd

The max_sd argument is deprecated. Please use max_fwhm instead.

min_rt

Minimum retention time.

max_rt

Maximum retention time.

min_fwhm

Minimum peak width, as a full width at half maximum, in the time units of the peak list. Peaks whose FWHM could not be measured (NA) are retained.

max_fwhm

Maximum peak width, as a full width at half maximum, in the time units of the peak list. Peaks whose FWHM could not be measured (NA) are retained.

converged

Logical. If TRUE, retains only peaks whose fit converged; if FALSE, retains only those that did not. A peak has converged == 0 either because the optimizer stopped short of convergence or because no optimizer ran at all, the latter occurring when the integration window held fewer points than the model has parameters. Requires a converged column, which peak lists made with fit = "raw" or before chromatographR 0.9.0 lack. Peaks whose converged is NA are retained.

window_limited

Logical. If FALSE, drops peaks whose fitted shape hit a limit set by the integration window or the sampling interval, meaning the window or the sampling rather than the data determined the reported shape; if TRUE, retains only those. Requires a window_limited column, which peak lists made with fit = "raw" or before chromatographR 0.9.0 lack. Peaks whose window_limited is NA are retained.

Value

A filtered peak_list object containing only peaks that satisfy the specified criteria. The call is appended to the filters attribute, as a line of code with numbers to 15 significant digits; print shows it, and get_peaktable copies it into args$filters.

Note

The structure of filter_peaks is adapted from the filterPeaks function in Ron Wehrens' alsace package.

See also

get_peaks, filter_peaktable

Author

Ron Wehrens, Ethan Bass

Examples

data(Sa_warp)
pks <- get_peaks(Sa_warp[1], lambda = "210")
filter_peaks(pks, min_height = 100)
#> A peak_list with 1 samples and 1 wavelength(s) (210 nm)
#> Fit method: egh | Time unit: min
#> Filtered with: filter_peaks(min_height = 100)
#> Total peaks: 8 (mean 8 per sample)
#> Source: Sa_warp[1]
filter_peaks(pks, converged = TRUE, window_limited = FALSE)
#> A peak_list with 1 samples and 1 wavelength(s) (210 nm)
#> Fit method: egh | Time unit: min
#> Filtered with: filter_peaks(converged = TRUE, window_limited = FALSE)
#> Total peaks: 27 (mean 27 per sample)
#> Source: Sa_warp[1]