Summarize peaks

Source: R/peak_mapping.R

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(...)

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

# S3 method for 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()