filterIdentificationDataFrame {MSnbase} | R Documentation

## Filter out unreliable PSMs.

### Description

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()`.

### 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`.

### Value

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

### Author(s)

Laurent Gatto

[Package MSnbase version 2.20.1 Index]