Description Usage Arguments Author(s) See Also Examples
View source: R/ProteinGroup-class.R
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,
1 2 3 | 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
1 2 3 4 5 6 | 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)
|
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