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Filter Non-reproducible ions

Source: R/filters.R
filter_cv.Rd

filter_cv() removes feature ions that are found to be non-reproducible between technical injection replicates. Reproducibility is assessed via mean or median coefficient of variation (CV) between technical replicates. As such, this filter is expecting an input dataset with at least two replicate injections per sample.

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_cv(mpactr_object, cv_threshold = NULL, cv_param, copy_object = FALSE)

Arguments

mpactr_object

An mpactr_object. See import_data().

cv_threshold

Coefficient of variation threshold. A lower cv_threshold will result in more stringent filtering and higher reproducibility. Recommended values between 0.2 - 0.5.

cv_param

Coefficient of variation (CV) statistic to use for filtering Options are "mean" or "median", corresponding to mean and median CV, respectively.

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_cv(data,
  cv_threshold = 0.01,
  cv_param = "mean",
  copy_object = TRUE
)
#> ℹ Parsing 1303 peaks for replicability across technical replicates.
#> ✔ 1298 ions failed the cv_filter filter, 5 ions remain.

data_filter <- filter_cv(data,
  cv_threshold = 0.01,
  cv_param = "median",
  copy_object = TRUE
)
#> ℹ Parsing 1303 peaks for replicability across technical replicates.
#> ✔ 1298 ions failed the cv_filter filter, 5 ions remain.