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Parse the PTM probabilities from Proteome Discoverer and add new columns with PTM information

parse_PTM_scores_pd.Rd

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

Arguments

obj

SummarizedExperiment. Proteomics dataset

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

SummarizedExperiment