mpactr (version 0.2.1)

filter_mispicked_ions: Mispicked ions filter

Description

filter_mispicked_ions() identifies ions that were incorrectly split into separate features during preprocessing. This filter checks the feature table for similar ions in terms of mass and retention time. Peaks found to be similar are merged into a single feature given merge_peaks is TRUE.

The parameter ringwin is the detector saturation mass window, specific for some instruments, such as Waters Synapse G2-Si-Q-ToF, to account for high concentration samples.

Parameter isowin is the isotopic mass window, which accounts for isotopic peaks of the same precussor mass that were incorrectly assigned during preprocessing.

copy_object: mpactr is built on an R6 class-system, meaning it operates on reference semantics in which data is updated in-place. Compared to a shallow copy, where only data pointers are copied, or a deep copy, where the entire data object is copied in memory, any changes to the original data object, regardless if they are assigned to a new object, result in changes to the original data object. We recommend using the default copy_object = FALSE as this makes for an extremely fast and memory-efficient way to chain mpactr filters together; however, if you would like to run the filters individually with traditional R style objects, you can set copy_object to TRUE as shown in the filter examples.

Usage

filter_mispicked_ions(
  mpactr_object,
  ringwin = 0.5,
  isowin = 0.01,
  trwin = 0.005,
  max_iso_shift = 3,
  merge_peaks = TRUE,
  merge_method = "sum",
  copy_object = FALSE
)

Value

an mpactr_object.

Arguments

mpactr_object

An mpactr_object. See import_data().

ringwin

Ringing mass window or detector saturation mass window. Default = 0.5 atomic mass units (AMU).

isowin

Isotopic mass window. Default = 0.01 AMU.

trwin

A numeric denoting the retention time threshold for assessing if ions should be merged. Default = 0.005.

max_iso_shift

A numeric. Default = 3.

merge_peaks

A boolean parameter to determine if peaks found to belong to the same ion should be merged in the feature table.

merge_method

If merge_peaks is TRUE, a method for how similar peaks should be merged. Can be one of "sum".

copy_object

A boolean parameter that allows users to return a copied object instead of modifying the object.

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,
  merge_method = "sum"
)