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Filter peak table

Source: R/filter_peaks.R
filter_peaktable.Rd

Filters features (columns) in a peak_table. Filtering is applied consistently across all components of the peak table, including the intensity matrix (tab), feature metadata (pk_meta), and reference spectra (if present). Filtering can be based on retention time, wavelength, feature intensity summarized across samples (mean, median, or max), feature sparsity (i.e., proportion of zero values across samples), and/or fit convergence.

Usage

filter_peaktable(
  peak_table,
  rts,
  min_rt,
  max_rt,
  min_value,
  max_zeros,
  lambda,
  min_converged,
  what = c("median", "mean", "max"),
  tol = 0
)

Arguments

peak_table

A peak_table object from get_peaktable.

rts

Vector of retention times used to select features. Values are mapped to the closest retention times in the peak table. If no match is found within tol, the value is ignored and a warning is issued. Cannot be combined with min_rt or max_rt.

min_rt

Minimum retention time for features to be retained.

max_rt

Maximum retention time for features to be retained.

min_value

Minimum threshold for feature intensity summarized across samples (using the method specified by what).

max_zeros

Maximum allowed feature sparsity (proportion of zero values across samples).

lambda

Wavelength(s) used to select features in the peak table. Only features matching the specified wavelength(s) are retained.

min_converged

Minimum value of the converged row of pk_meta, between 0 and 1. That row summarizes converged over the peaks in each feature by the summarize_by method given to get_peaktable: with "mean", it is the proportion of those peaks whose fit converged, so 0.8 retains features that converged in at least 80% of them; with the default "weighted.mean", that proportion is weighted by peak intensity. Requires a converged row in pk_meta, so it is unavailable for peak tables built from fit = "raw" peak lists.

what

Method used to summarize feature intensity across samples for filtering. One of "mean", "median" (default), or "max".

tol

Tolerance for matching of retention times to rts. A feature is considered a match if the absolute difference is at most tol. Defaults to 0, which requires an exact match.

Value

A filtered peak_table containing only features (columns) that satisfy the specified criteria. The same feature indices are applied to all peak_table components. The call is appended to args$filters, as a line of code with numbers to 15 significant digits.

See also

get_peaktable, filter_peaks

Author

Ethan Bass

Examples

data(pk_tab)
pk_tab <- filter_peaktable(pk_tab, min_rt = 10, max_rt = 16)