Keep only those proteins with 2 IDENTIFIED peptides

Keep only those proteins with 2 IDENTIFIED peptides

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(), normalize_log2_robscale(), robust_scale(), scale_with_subset(), scale_with_subset_by_factors()

Examples

istar <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
filterPep <- prolfqua::filter_proteins_by_peptide_count( istar$data ,  istar$config )
#> Column added : nr_peptide_Id_IN_protein_Id
x <- prolfqua::summarize_hierarchy(filterPep$data , istar$config)
stopifnot(x$peptide_Id_n >= istar$config$parameter$min_peptides_protein)