Filter Insource ions

filter_insource_ions() identifies and removes in-source ion clusters based on a Pearson correlation threshold. Groups of co-eluting features with identical retention time are identified and used to generate Pearson correlation matrices. Clusters with self-similarity greater than the user-defined cluster_threshold within these matrices are identified as likely belonging to a single precursor ion and is associated insource ion. Highly correlated ions are identified and removed.

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_insource_ions(
  mpactr_object,
  cluster_threshold = 0.95,
  copy_object = FALSE
)

Arguments

mpactr_object

An mpactr_object. See import_data().

cluster_threshold

Cluster threshold for ion deconvolution. Default = 0.95.

copy_object

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

Value

an mpactr_object

Examples

data <- import_data(
  example_path("coculture_peak_table.csv"),
  example_path("metadata.csv"),
  format = "Progenesis"
)

data_filter <- filter_insource_ions(data,
  cluster_threshold = 0.95
)
#> ℹ Parsing 1303 peaks for insource ions.
#> ✔ 71 ions failed the insource filter, 1232 ions remain.