subsetIBSpectra {isobar} | R Documentation

## Subset IBSpectra objects

### Description

Returns an IBSpectra object which is a subset of the input, excluding or exclusively containing the peptides or proteins supplied.

### Usage

    subsetIBSpectra(x, protein = NULL, peptide = NULL,
                    direction = "exclude",
                    specificity = c(REPORTERSPECIFIC, GROUPSPECIFIC, UNSPECIFIC), ...)

### Arguments

`x` | IBSpectra object.
`protein` | Protein group identifiers. Use `protein.g` to get protein group identifiers from protein database ACs.
`peptide` | Peptide sequences.
`direction` | either 'include' or 'exclude'.
`specificity` | When 'protein' is supplied: Which peptides should be selected? See `specificities`.
`...` | Further arguments passed to `spectrumSel`

### Author(s)

Florian P Breitwieser

### See Also

`protein.g`, `spectrumSel`, `specificities`

### Examples

    data(ibspiked_set1)

    # get Keratin proteins
    keratin.proteins <- protein.g(proteinGroup(ibspiked_set1),"Keratin")

    # exclude Keratin proteins
    subsetIBSpectra(ibspiked_set1,protein=keratin.proteins,direction="exclude")

[Package isobar version 1.28.1 Index]