isobar (version 1.18.0)

spectra.count2: 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

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)