observedKnownSites: Observed modification sites.

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

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?

Author(s)

Florian P. Breitwieser

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")

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