mpactr (version 0.3.1)

qc_summary: Summary of Filtering

Description

Parses an mpactr object and extracts 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 quality ions. Ions tagged as group, mispicked, replicability, or ionsource were removed during the corresponding filter.

Usage

qc_summary(mpactr_object)

Value

a data.table reporting the number of high quality ions ("Passed") or the filter in which they were removed.

Arguments

mpactr_object

an mpactr_object.

Examples

 # \dontshow{
limit_cores()
# }
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
)

summary <- qc_summary(data_filter)
summary