filterIdentificationDataFrame: Filter out unreliable PSMs.
In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description Usage Arguments Details Value Author(s)

View source: R/functions-addIdentificationData.R

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()
)

`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()`.

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.

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

Laurent Gatto

MSnbase documentation built on Jan. 23, 2021, 2 a.m.