spectra.count2: Spectral count for peptides and proteins in ProteinGroup...

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

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)

isobar documentation built on Nov. 8, 2020, 7:48 p.m.