Filter Ions by Group

Usage

filter_group(
  mpactr_object,
  group_threshold = 0.01,
  group_to_remove,
  remove_ions = TRUE,
  copy_object = FALSE
)

Arguments

mpactr_object: An mpactr_object. See import_data().
group_threshold: Relative abundance threshold at which to remove ions. Default = 0.01.
group_to_remove: Biological group name to remove ions from.
remove_ions: A boolean parameter. If TRUE failing ions will be removed from the peak table. Default = TRUE.
copy_object: A boolean parameter that allows users to return a copied object instead of modifying the object.

Value

an mpactr_object.

Details

filter_group() removes feature ions that are present in a user-defined group based on a relative abundance threshold. This could be particularly useful to filter out features found present in solvent blank samples. Further, this filter can be ultilized to remove features in media blank sample for experiments on microbial cultures. The presence or absence of features in a group of samples is determined by first averaging injection replicates and then averaging biological replicates within each biological treatment group. A feature is present in a group if its abundance is greater than the user-defined group_threshold. The default is 0.01, meaning a feature is removed if its abundance is 1% of that in the sample group in which it is most abundant. For example, blank filtering can remove features whose mean abundance in solvent blank injections is greater than 1% of their maximum mean abundance in experimental samples.

If you would like to remove features found in media blank samples, we recommend testing the group_threshold parameter.

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.

Examples

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

data_filter <- filter_group(data,
  group_threshold = 0.01,
  group_to_remove = "Blanks",
  remove_ions = TRUE
)
#> ℹ Parsing 1303 peaks based on the sample group: Blanks.
#> ℹ Argument remove_ions is: TRUE.Removing peaks from Blanks.
#> ✔ 796 ions failed the Blanks filter, 507 ions remain.