peptides_inReference: Peptide Reference Merger

In rr-2/PeptideRanger:

Peptide Reference Merger

Description

Matches peptide reference information with peptidome sequences

Usage

peptides_inReference(
  peptidome,
  pep_reference,
  reference_name,
  exp_counts_col,
  detection_freq,
  detection_ratio
)

Arguments

peptidome	list of all possible peptides for proteins of interest and their uniprot IDs
pep_reference	dataframe with a "sequence" column of peptides and a column of n observations in a reference
reference_name	the name of the reference, which is used to label the output columns
exp_counts_col	the name of the reference column containing the n of peptide observations
detection_freq	If TRUE, calculates the each peptide's frequency of appearance in the reference
detection_ratio	If TRUE, calculates ratio of peptide observations to parent protein observations

Value

dataframe of peptidome with reference information

Examples

## Not run: 

peptides_inReference(peptidome = SwissProt2018_peptidome,
                     pep_reference = tm_peptides,
                     reference_name = "transmembrane")

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

## End(Not run)

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