observedKnownSites {isobar} | R Documentation |
Functions to display the modification sites observed for each protein isoform and count the number of modified residues per protein.
observedKnownSites(protein.group, protein.g, ptm.info, modif, modification.name = NULL) modif.site.count(protein.group, protein.g = reporterProteins(protein.group), modif, take = max) modif.sites(protein.group, protein.g = reporterProteins(protein.group), modif)
protein.group |
ProteinGroupb object. |
protein.g |
protein group identifier. |
ptm.info |
ptm information data.frame, see ?getPtmInfo. |
modif |
Modification to track, e.g. 'PHOS'. |
modification.name |
Value to filter 'modification.name' column in ptm.info. |
take |
should be either max or min: When multiple isoforms are present, which value should be taken for the count? |
Florian P. Breitwieser
data(ib_phospho) data(ptm.info) # Modification sites of reporter proteins: # a list of protein groups, # containing sub-lists of identified sites for each isoform protein.modif.sites <- sort(modif.site.count(proteinGroup(ib_phospho),modif="PHOS")) # Details on modification sites of proteins # detected with most modifications modif.sites(proteinGroup(ib_phospho),modif="PHOS",protein.g=names(tail(protein.modif.sites))) # How many sites are known, and how many known sites have been observed? observedKnownSites(proteinGroup(ib_phospho),modif="PHOS",protein.g=names(tail(protein.modif.sites)),ptm.info=ptm.info,modification.name="Phospho")