mzIDpeptides-class: A class to store peptide information from an mzIdentML file

Description Usage Arguments Details Methods (by generic) Slots Objects from the class See Also

Description

This class handles parsing and storage of peptide information from mzIDentML files, residing at the /x:MzIdentML/x:SequenceCollection/x:Peptide node.

Usage

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## S4 method for signature 'mzIDpeptides'
show(object)

## S4 method for signature 'mzIDpeptides'
length(x)

## S4 method for signature 'mzIDpeptides'
peptides(object, safeNames = TRUE)

## S4 method for signature 'mzIDpeptides'
modifications(object)

Arguments

object

An mzIDpeptides object

x

An mzIDpeptides object

safeNames

Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The information is stored in a dataframe with an id, an optinal name and the amino acid sequence of the peptide. Alongside a list is stored with modification information of each peptide. Each row in the dataframe has a corresponding entry en the list. If no modification of the peptide is present the entry is NULL, if a modification is present the entry is a dataframe, listing the different modifications of the peptide.

Methods (by generic)

  • show: Short summary of the content of the object

  • length: Report the number of peptides

  • peptides: Get the peptides identified.

  • modifications: Get the modification on the identified peptides

Slots

peptides

A data.frame containing all peptides used in the search

modifications

A list containing possible modifications of the peptides listed in @peptides

Objects from the class

Objects of mzIDpeptides are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDpeptides.

See Also

mzIDpeptides

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDdatabase-class, mzIDevidence-class, mzIDparameters-class, mzIDpsm-class



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