Filter out unreliable PSMs. — filterIdentificationDataFrame • MSnbase

A function to filter out PSMs matching to the decoy database, of rank greater than one and matching non-proteotypic peptides.

Usage

filterIdentificationDataFrame(
  x,
  decoy = "isDecoy",
  rank = "rank",
  accession = "DatabaseAccess",
  spectrumID = "spectrumID",
  verbose = isMSnbaseVerbose()
)

Arguments

x: A data.frame containing PSMs.
decoy: The column name defining whether entries match the decoy database. Default is "isDecoy". The column should be a logical and only PSMs holding a FALSE are retained. Ignored is set to NULL.
rank: The column name holding the rank of the PSM. Default is "rank". This column should be a numeric and only PSMs having rank equal to 1 are retained. Ignored is set to NULL.
accession: The column name holding the protein (groups) accession. Default is "DatabaseAccess". Ignored is set to NULL.
spectrumID: The name of the spectrum identifier column. Default is spectrumID.
verbose: A logical verbosity flag. Default is to take isMSnbaseVerbose().

Value

A new data.frame with filtered out peptides and with the same columns as the input x.

Details

The PSMs should be stored in a data.frame such as those produced by readMzIdData(). Note that this function should be called before calling the reduce method on a PSM data.frame.

Author

Laurent Gatto