Filter Peak Table — filter_peak

This function is a wrapper for all of mpactr's filter functions. When called with a list of parameters that was generated from one of the following functions, it will call the subsequent filter: filter_mispicked_ions_params(), filter_group_params(), filter_cv_params(), and filter_insource_ions_params(). You can also find more information on these functions inmpactr documentation.

Usage

filter_peak_table(mpactr_object, params)

# S3 method for class 'filter_mispicked_ions'
filter_peak_table(mpactr_object, params)

# S3 method for class 'filter_group'
filter_peak_table(mpactr_object, params)

# S3 method for class 'filter_cv'
filter_peak_table(mpactr_object, params)

# S3 method for class 'filter_insource_ions'
filter_peak_table(mpactr_object, params)

Arguments

mpactr_object: the mpactr_object is an object generated from the import_all_data() function. This is how we begin our pipeline.
params: the list of arguments generated from calling one of these functions: filter_mispicked_ions_params(), filter_group_params(), filter_cv_params(), and filter_insource_ions_params().

Value

a mpactr object that has been filter based on the supplied parameters.

Examples

data.table::setDTthreads(threads = 1)
data <-
   import_all_data(peak_table =
                   mums2::mums2_example("botryllus_pt_small.csv"),
                   metadata =
                   mums2::mums2_example("boryillus_metadata.csv"),
                   format = "None")
filtered_data <- data |>
   filter_peak_table(filter_mispicked_ions_params())
#> ℹ Checking 349 peaks for mispicked peaks.
#> ℹ Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
#> ✔ 1 ions failed the mispicked filter, 348 ions remain.