spectra.count2 {isobar} | R Documentation |
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,
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, ...)
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 |
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 |
Florian P Breitwieser
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)