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Filter Peak Table

Source: R/filter.R
filter_peak_table.Rd

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 <-
   import_all_data(peak_table =
                   mums2::mums2_example("botryllus_pt_small.csv"),
                   meta_data =
                   mums2::mums2_example("meta_data_boryillus.csv"),
                   format = "None")
#> If peak table has corrupted compound names they will be converted to
#>       utf-8 and if there are any commas, they will be converted to periods(.).
filtered_data <- data |>
   filter_peak_table(filter_mispicked_ions_params()) |>
   filter_peak_table(filter_cv_params(cv_threshold = 0.2)) |>
   filter_peak_table(filter_group_params(group_threshold = 0.1,
                                             "Blanks")) |>
   filter_peak_table(filter_insource_ions_params())
#> ℹ Checking 1500 peaks for mispicked peaks.
#> ℹ Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
#> ✔ 50 ions failed the mispicked filter, 1450 ions remain.
#> ℹ Parsing 1450 peaks for replicability across technical replicates.
#> ✔ 329 ions failed the cv_filter filter, 1121 ions remain.
#> ℹ Parsing 1121 peaks based on the sample group: Blanks.
#> ℹ Argument remove_ions is: TRUE.Removing peaks from Blanks.
#> ✔ 342 ions failed the Blanks filter, 779 ions remain.
#> ℹ Parsing 779 peaks for insource ions.
#> ✔ 55 ions failed the insource filter, 724 ions remain.