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.

iso_summarize_peak_mappings(dt, file_id = default(file_id),
  compound = default(compound), rt = default(rt))

Arguments

dt

data frame with peak data

file_id

the column(s) in dt that uniquely identify a file/set of peaks that belong together

compound

the column in peak_maps that holds compound information

rt

the column in dt and colum prefix in peak_maps ("rt:...") that holds retention time information

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