ComputeFDR

Usage: java -Xmx500M -cp MSGFDB.jar fdr.ComputeFDR 
	 -f resuleFileName protCol decoyPrefix or -f targetFileName decoyFileName
	 -i specFileCol (the specFile column number)
	 -n specIndexCol (the spectrum index column number)
	 -p pepCol (the peptide column number)
	 -s scoreCol 0/1 (0: smaller better, 1: greater better)
	 [-o outputFileName]
	 [-delim delimeter] (default: \t)
	 [-m colNum keyword (the column 'colNum' must contain 'keyword'. If 'keyword' is delimetered by ',' (e.g. A,B,C), then at least one must be matched.)]
	 [-h 0/1] (0: no header, 1: header (default))
	 [-fdr fdrThreshold (default: 1)]
	 [-pepfdr pepFDRThreshod (default: 1)]
	 [-decoy 0/1 (default: 0)]

Parameters:

  • -f resultFileName dbCol decoyPrefix
    • This parameter must be used when a result file contains both target and decoy Peptide-Spectrum Matches (PSMs).
    • FDR(t) = #decoy / #target
      • t: score
      • #decoy: number of decoy PSMs with score equal or better than t
      • #target: number of target PSMs with score equal or better than t
    • protCol: zero-based column number of protein id
    • decoyPrefix: prefix representing decoy ids (e.g. XXX for InsPecT, REV for MS-GFDB)
  • -f targetFileName decoyFileName
    • This parameter must be used when target and decoy PSMs are in separate files.
    • FDR(t) = #decoy / #target
      • t: score
      • #decoy: number of decoy PSMs with score equal or better than t
      • #target: number of target PSMs with score equal or better than t
  • -i specFileCol
    • specFileCol: zero-based column number of SpectrumFile (e.g. 0 for InsPecT)
  • -n specIndexCol
    • specIndexCol: zero-based column number of the spectrum index (e.g. 1 for InsPecT)
    • The spectrum index should identify a spectrum uniquely (e.g. Scan# column for InsPecT)
  • -p pepCol
    • pepCol: zero-based column number of peptide id (e.g. 2 for InsPecT)
  • -s scoreCol 0/1 (0: smaller better, 1: greater better)
    • scoreCol: zero-based column number of the score to be used for FDR calculation (e.g. 14 for InsPecT F-score)
    • 0/1: 0 if smaller scores are better (e.g. p-value, E-value, FDRs, etc.), 1 otherwise (e.g. MQScore, Xcorr, F-score, etc.)
  • -o outputFileName (default: stdout)
    • outputFileName: file name where output will be written to
  • -delim delimeter (default: \t)
    • delimeter: delimeter separating columns (e.g. "\t" for InsPecT)
  • -m colNum keyword
    • colNum: zero-based column number
    • keyword: keyword where the specified column must contain - if 'keyword' is delimetered by ',' (e.g. A,B,C), then at least one must be matched.
      E.g. -m 4 2,3 (consider only charge 2 or 3 spectra in InsPecT results).
  • -h 0/1 (0: no header, 1: header (default))
    • 0/1: if 1, the first line of input file(s) is considered as a header
  • -fdr fdrThreshold
    • fdrThreshold: if specified, only PSMs with FDRs smaller then fdrThreshold will be printed out
  • -pepfdr pepFDRThreshold
    • pepFDRThreshold: if specified, only PSMs with peptide level FDRs smaller then pepFDRThreshold will be printed out
  • -decoy 0/1 (Default: 0)
    • 0/1: if 0, only target PSMs are written to the output. If 1, both target and decoy PSMs are written to the output.

Example:

  • java -Xmx2000M -cp MSGFDB.jar fdr.ComputeFDR -f msgfdb.tsv.temp.tsv 8 REV -i 0 -n 1 -p 7 -s 11 0 -o msgfdb.tsv
    • Takes MS-GFDB output "msgfdb.temp.tsv", add FDR columns (FDR and PepFDR) to the results and save it to msgfdb.tsv.
  • java -Xmx2000M -cp MSGFDB.jar fdr.ComputeFDR -f inspect.out 3 XXX -i 0 -n 1 -p 2 -s 14 1 -fdr 0.05 -o inspectWithFDR.out
    • Takes "inspect.out", computes spectrum and peptide level FDRs using F-scores, and writes PSMs whose FDRs are smaller than or equal to 0.05 to inspectWithFDR.out file.
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