peptide.count {isobar} | R Documentation

## Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.

### Description

Report the peptide count, spectral count and sequence coverage for supplied proteins.

### Usage

    peptide.count(protein.group, protein.g = reporterProteins(protein.group),
                  specificity = c("reporter-specific", "group-specific", "unspecific"), ...)

    spectra.count(protein.group, protein.g = reporterProteins(protein.group),
                  specificity = c("reporter-specific", "group-specific", "unspecific"),
                  modif = NULL, ...)

    sequence.coverage(protein.group, protein.g = reporterProteins(protein.group),
                      specificity = c("reporter-specific", "group-specific", "unspecific"),
                      simplify = TRUE, ...)

### Arguments

`protein.group` | ProteinGroup object.
`protein.g` | Protein group identifier.
`specificity` | Specificity of peptides.
`modif` | Only count peptides having a certain modification.
`simplify` | If simplify=TRUE, a named numeric vector is returned, with the mean sequence coverage of the ACs of each protein.g supplied. Else, a list with the length of protein.g is returned having the sequence coverage for each protein AC.
`...` | Further arguments to `peptides`

### Author(s)

Florian P Breitwieser

### See Also

`calculate.emPAI`, `calculate.dNSAF`, `ProteinGroup`

### Examples

      data(ibspiked_set1)
      sc <- spectra.count(proteinGroup(ibspiked_set1))
      pc <- peptide.count(proteinGroup(ibspiked_set1))
      plot(jitter(sc),jitter(pc),log="xy")

[Package isobar version 1.38.0 Index]