observedKnownSites {isobar} | R Documentation

## 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?

### 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")

[Package isobar version 1.28.1 Index]