Keep only those proteins with 2 IDENTIFIED peptides

Keep only those proteins with 2 IDENTIFIED peptides

Usage

filter_proteins_by_peptide_count(pdata, config)

Arguments

pdata

data.frame

config

AnalysisConfiguration

Value

list with data.frame (data) and name of new column (name)

See also

Other preprocessing: INTERNAL_FUNCTIONS_BY_FAMILY, apply_to_response_matrix(), get_robscales(), 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
lfq <- LFQData$new(istar$data, istar$config)
filterPep <- prolfqua::filter_proteins_by_peptide_count(istar$data, istar$config)
#> Column added : nr_peptide_Id_IN_protein_Id
x <- prolfqua::summarize_hierarchy(filterPep$data,
  lfq$hierarchy_keys(), lfq$isotope_label())
stopifnot(x$peptide_Id_n >= istar$config$min_peptides_protein)
#> Warning: Unknown or uninitialised column: `peptide_Id_n`.