isobar (version 1.18.0)

observedKnownSites: Observed modification sites.

Description

Functions to display the modification sites observed for each protein isoform and count the number of modified residues per protein.

Usage

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)

Arguments

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?

Examples

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")