iso_summarize_peak_mappings: Summarize peaks

In KopfLab/isoprocessorCUB: IRMS data processor

Description

Summarize peaks after peak mapping. This function is called after iso_map_peaks and can be used in combination with iso_get_problematic_peaks to inspect problematic peaks in particular. For the file_id parameter, make sure to use the same set or a subset of the columns used to identify individual files in the iso_map_peaks call before.

Usage

iso_summarize_peak_mappings(...)

## S3 method for class 'iso_file_list'
iso_summarize_peak_mappings(
  iso_files,
  include_file_info = NULL,
  compound = default(compound),
  rt = default(rt)
)

## S3 method for class 'data.frame'
iso_summarize_peak_mappings(
  peak_table,
  file_id = default(file_id),
  compound = default(compound),
  rt = default(rt)
)

Arguments

...	S3 method placeholder parameters, see class specific functions for details on parameters
iso_files	collection of continuous flow iso_file objects
include_file_info	which file information to include (see iso_get_file_info). Use c(...) to select multiple, supports all select syntax including renaming columns.
compound	the column in peak_maps that holds compound information
rt	the column in peak_table and colum prefix in peak_maps ("rt:...") that holds retention time information
peak_table	data frame with the peak table
file_id	the column(s) in peak_table that uniquely identify a file/set of peaks that belong together

Value

summary data table with one row for each unique combination of the file_id parameter

• mapped: number of peaks that were identified during the mapping process (out of the total number of peaks in each sample)

• ambiguous: number of mapped peaks that were ambiguous (out of all the mapped peaks) because they either have multiple matches or because they overlap with other mapped peaks

• missing: number of peaks that were listed in the peak map but appear to be missing in the sample (out of the total number of peaks listed in the peak map)

• peak_info: concatenated text with all the peaks and their retention times (with '?' for unknown peak names, retention times or other ambiguities

See Also

Other peak mapping functions: iso_get_problematic_peaks(), iso_map_peaks(), iso_remove_problematic_peak_mappings()

KopfLab/isoprocessorCUB documentation built on Nov. 8, 2021, 9:54 a.m.