read psm.tsv produced by FragPipe and convert into long format

Usage

tidy_FragPipe_psm_V2(
  psm_files,
  purity_threshold = 0.5,
  PeptideProphetProb = 0.9,
  abundance_threshold = 0,
  quan_column_prefix = "^Intensity",
  aggregate = TRUE
)

Arguments

psm_files: path(s) to psm.tsv file(s)
purity_threshold: purity threshold default = 0.5
PeptideProphetProb: default 0.9
abundance_threshold: minimum abundance threshold
quan_column_prefix: regex prefix for quantitative columns
aggregate: aggregate spectra to psm level