isobar (version 1.18.0)

ProteinGroup-class: ProteinGroup objects

Description

The ProteinGroup class is a container for identified peptides and proteins, and groups them to distinguish proteins with specific peptides.

Usage

ProteinGroup(from,template=NULL,proteinInfo=data.frame())
protein.ac(x, protein.g)
protein.g(x, pattern, variables=c("AC","name"), ...)

Arguments

from

data.frame object to create a ProteinGroup from. See Details from column specifications

template

'template' ProteinGroup object for grouping.

x

ProteinGroup object

protein

character string

proteinInfo

data.frame for proteinInfo slot

protein.g

character string, denoting a 'protein group'.

pattern

character string, see grep for details.

variables

AC maps a protein accession code to a protein group. name maps using protein information from proteinInfo.

...

Passed on to grep.

Constructor

ProteinGroup(tbl.prot.pep,template=NULL): Creates a ProteinGroup object.

tbl.prot.pep

A 'data.frame' with three columns: 1. Protein, 2. Peptide, 3. Spectrum.

template

Optional ProteinGroup object the grouping is based upon.

Coercion

In the code snippets below, x is a ProteinGroup object.

as(from, "ProteinGroup"):

Creates a ProteinGroup object from a data.frame.

as.data.frame(x, row.names = NULL, optional = FALSE):

Creates a data.frame with columns protein (character), peptide (character), spectrum.

as.concise.data.frame(from):

Creates a 'concise' data.frame with one spectrum per row, and protein ACs combined

Accessors

In the following code snippets, x is a ProteinGroup object.

spectrumToPeptide(x):

Gets spectrum to peptide assignment.

peptideInfo(x):

Peptide information such as protein start position.

peptideSpecificity(x):

Gets a 'data.frame' containing the peptide specificity: they can be reporter-specific, group-specific, or non-specific.

peptideNProtein(x):

Gets peptide to protein assignment.

indistinguishableProteins(x):

Gets the proteins which cannot be distinguished based on peptide evidence.

proteinGroupTable:

Gets the protein grouping, listing reporters and group members.

peptides(x,protein=NULL,specificity=c("reporter-specific", "group-specific","unspecific"),columns="peptide",set=union):

Gets all peptides detected, or just those for a protein with the defined specificity. columns might define multiple columns of peptideSpecificity(x). set=union returns the union of peptides of all proteins defined, set=intersect returns the intersection.

Details

The ProteinGroup class stores spectrum to peptide to protein mapping. The proteins are grouped by their evidence, i. e. peptides:

• Peptides with changes only from Leucin to Isoleucin are considered the same, as they cannot be distinguished by MS.
• Proteins which are detected with the same peptides are grouped together to a 'indistinguishable protein'- normally these are splice variants.
• Proteins with specific peptides are 'reporters'.
• Proteins with no specific peptides are grouped under these 'reporters.

This information is stored in six slots:

spectra.n.peptides

a named 'character' vector, names being spectrum identifier and values are peptides.

peptide.n.proteins

a 'data.frame' containing the number of proteins the peptides could derive from.

peptide.n.protein

a character 'matrix' linking peptides to proteins.

indistinguishable.proteins

a 'matrix' contain.

See Also

IBSpectra

Examples

tbl <- data.frame(spectrum=1:14,peptide=c(rep(letters[1:3],4),"a","x"),
                  modif=":",start.pos=1,
                  protein=c(rep(c("A","B"),each=6),"C","D"))
pg <- ProteinGroup(tbl)
pg
proteinGroupTable(pg)

data(ibspiked_set1)
pg <- proteinGroup(ibspiked_set1)
ceru.proteins <- protein.g(pg,"CERU")

## all ceru peptides
peptides(pg,ceru.proteins)

## peptides shared by all ceru proteins
peptides(pg,ceru.proteins, set=intersect)