spectra.count2 {isobar} | R Documentation

## Spectral count for peptides and proteins in ProteinGroup objects.

### Description

Spectral count for peptides and proteins in ProteinGroup objects. It can - other than `spectra.count` - quantify the spectra count on the level of peptides, potenitally modifed, too,

### Usage

    spectra.count2(ibspectra, value = reporterProteins(protein.group),
                   type = "protein.g", specificity = c("reporter-specific", "group-specific", "unspecific"),
                   modif = NULL, combine = FALSE, subset = NULL, require.quant = NULL, ...)

### Arguments

`ibspectra` | IBSpectra object.
`value` | List of protein group identifiers or peptides.
`type` | Either 'protein.g' or 'peptide'.
`specificity` | Specificity of peptides.
`modif` | Only count peptides having a certain modification.
`combine` | If TRUE, only one combined result is returned.
`subset` | Allows to specify an `expression` to subset `link{featureData}` of the ibspectra.
`require.quant` | If not NULL, it may be 'any' or 'all' to only consider spectra with quantitative information in at least one or all channels.
`...` | Further arguments to `peptides`

### Author(s)

Florian P Breitwieser

### See Also

`spectra.count`, `ProteinGroup`

### Examples

      data(ibspiked_set1)
      pg <- proteinGroup(ibspiked_set1)
      protein.gs <- protein.g(pg,"CERU")
      sc <- spectra.count2(ibspiked_set1,protein.gs)
      sc.ik <- spectra.count2(ibspiked_set1,protein.gs,modif="iTRAQ4plex_K")
      rbind(spectra.counts=sc,spectra.counts_iTRAQk=sc.ik)

[Package isobar version 1.34.0 Index]