prioritize_peptides: Peptide Prioritizer

In rr-2/PeptideRanger:

Peptide Prioritizer

Description

Selects the top n peptides for a list of protein uniprot IDs given a set of priorities

Usage

prioritize_peptides(
  uniprot_list,
  max_n,
  peptidome,
  prediction_model,
  priorities,
  priority_thresholds
)

Arguments

uniprot_list	a list of uniprot IDs for proteins of interest
max_n	max number of peptides selected for each protein
peptidome	list of all possible peptides for relevant proteome, their uniprot IDs, and the values for their non-RF priorities
prediction_model	RF model used to predict scores for peptide detectability
priorities	list of priority column names in peptidome
priority_thresholds	list of minimum values that priorities must reach to be considered

Value

list of n prioritized peptides for proteins of interest

Examples

## Not run: 
prioritize_peptides(uniprot_list = c("Q9NQ94", "P04217", "A8K2U0"),
                    peptidome = SwissProt2018_peptidome,
                    prediction_model = CPTAC_RFmodel,
                    priorities = "RF_score",
                    priority_thresholds = 0)


CPTAC_peptidome <- peptides_inReference(peptidome = SwissProt2018_peptidome,
                                        reference_name = "CPTAC",
                                        pep_reference = CPTAC_exp_counts,
                                        exp_counts_col = "n_obs_pep",
                                        detection_freq = TRUE)

prioritize_peptides(uniprot_list = c("Q3T906", "P04217", "A8K2U0"),
                    max_n = 10, peptidome = CPTAC_peptidome,
                    prediction_model = RFmodel_CPTAC,
                    priorities = c("CPTAC_freq","RF_score"),
                    priority_thresholds = c(0.8, 0))

## End(Not run)

rr-2/PeptideRanger documentation built on May 27, 2023, 4:43 p.m.