Description Usage Arguments Value See Also
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
)
|
... |
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 |
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 |
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
Other peak mapping functions:
iso_get_problematic_peaks()
,
iso_map_peaks()
,
iso_remove_problematic_peak_mappings()
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