Keep only the proteins with enough peptides

Keeps the rows of the proteins with at least `config$min_peptides_protein` children at the next hierarchy level, counted by [nr_B_in_A()], and adds that count. The package dataset `data_ionstar` calls it from its `filtered()` method.

Usage

filter_proteins_by_peptide_count(pdata, config)

Arguments

pdata

data.frame in the long format of `config`

config

AnalysisConfiguration

Value

list with the filtered `data` and the `name` of the count column, `NULL` when the hierarchy has no child level

See also

Other preprocessing: INTERNAL_FUNCTIONS_BY_FAMILY, apply_to_response_matrix(), get_robscales(), nr_B_in_A(), robust_scale(), scale_with_subset()

Examples

istar <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
filtered <- prolfqua:::filter_proteins_by_peptide_count(istar$data, istar$config)
stopifnot(all(filtered$data[[filtered$name]] >= istar$config$min_peptides_protein))