Parse the PTM probabilities and add new columns with PTM information

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

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