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

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

Arguments

x A data.frame containing PSMs. 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. 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. The column name holding the protein (groups) accession. Default is "DatabaseAccess". Ignored is set to NULL. The name of the spectrum identifier column. Default is spectrumID. 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.

Laurent Gatto