parse_PTM_scores: Parse the PTM probabilities and add new columns with PTM...

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Parse the PTM probabilities and add new columns with PTM information

Description

Extract PTM information from the PTM probabilities column in the output from PD and add new columns with this information. Also optionally prints a summary of how many features (PSMs/peptides) pass a given probability threshold

Usage

parse_PTM_scores(
  obj,
  threshold = 95,
  ptm_col = "PhosphoRS.Best.Site.Probabilities",
  prob_split = "; |: ",
  collapse_delimiter = ";",
  verbose = TRUE
)

Arguments

obj	data.frame with PD output at PSM/peptide level
threshold	numeric If any score is below a set threshold, disregard all putative PTM sites
ptm_col	character Columm name for PTM probabilities
prob_split	character regex to split PTM probabilities
collapse_delimiter	character delimiter for multiple values in output columns
verbose	Set TRUE to print log of events to console

Value

data.frame

CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.