Parses an mpactr object and exracts a summary of all applied filters. Specifically, the fate of each input ion is reported as ion status. Status options are: Passed, mispicked, group, replicability, and insouce. A status of Passed ions is returned for ions that passed all applied filters and therefore are expected to be high quaility ions. Ions tagged as group, mispicked, replicability, or ionsource were removed during the correspoding filter.
Value
a data.table reporting the number of high quality ions
("Passed") or the filter in which they were removed.
Examples
data <- import_data(
example_path("coculture_peak_table.csv"),
example_path("metadata.csv"),
format = "Progenesis"
)
data_filter <- filter_mispicked_ions(data,
ringwin = 0.5,
isowin = 0.01,
trwin = 0.005,
max_iso_shift = 3,
merge_peaks = TRUE
)
#> ℹ Checking 1303 peaks for mispicked peaks.
#> ℹ Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
#> ✔ 70 ions failed the mispicked filter, 1233 ions remain.
summary <- qc_summary(data_filter)
summary
#> status compounds
#> <char> <char>
#> 1: Passed 1
#> 2: Passed 10
#> 3: Passed 100
#> 4: Passed 1000
#> 5: Passed 1001
#> ---
#> 1299: mispicked 1267
#> 1300: mispicked 546
#> 1301: mispicked 495
#> 1302: mispicked 1289
#> 1303: mispicked 1290