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APAF-bioinformatics / ProteomeScholaR

GNU Lesser General Public License v3.0
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Add option to NOT filter by proteotypic peptide #37

Open Bucket-Chemist opened 1 week ago

Bucket-Chemist commented 1 week ago

srlQvalueProteotypicPeptideCleanHelper <- function(input_table , qvalue_threshold = 0.01 , global_qvalue_threshold = 0.01 , choose_only_proteotypic_peptide = 1 # need to change to > or = (currently boolean) , input_matrix_column_ids = c("Run" , "Precursor.Id" , "Protein.Ids" , "Stripped.Sequence" , "Modified.Sequence" , "Precursor.Charge" , "Precursor.Quantity" , "Precursor.Normalised") , protein_id_column = Protein.Ids , q_value_column = Q.Value , global_q_value_column = Global.Q.Value , proteotypic_peptide_sequence_column = Proteotypic) {

search_srl_quant_cln <- input_table |> dplyr::filter( {{q_value_column}} < qvalue_threshold & {{global_q_value_column}} < global_qvalue_threshold & {{proteotypic_peptide_sequence_column}} == choose_only_proteotypic_peptide ) |> dplyr::select(all_of( input_matrix_column_ids))

search_srl_quant_cln

}0

Bucket-Chemist commented 1 week ago

{{proteotypic_peptide_sequence_column}} >= choose_only_proteotypic_peptide