mzIDdatabase-class: A class to store database information from an mzIdentML file

In thomasp85/mzID: An mzIdentML parser for R

Description

This class handles parsing and storage of database information from mzIDentML files, residing at the /MzIdentML/SequenceCollection/DBSequence node.

Usage

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

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

## S4 method for signature 'mzIDdatabase'
database(object, safeNames = TRUE)

Arguments

object	An mzIDevidence object
x	An mzIDdatabase object
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The content of the class is stored in a data.frame with columns depending on the content of the mzIdentML file. Required information for files conforming to the mzIdentML standard are: 'accession', 'searchDatabase_ref' and 'id', while additional information can fx be 'length' (number of residues), 'description' (from the fasta file) and 'sequence' (the actual sequence).

Methods (by generic)

• show: Short summary of the content of the object

• length: Report the number of proteins in the database

• database: Get the database used for searching

Slots

database

A data.frame containing references to all the database sequences from the mzIdentML file

Objects from the class

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

See Also

mzIDdatabase

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

thomasp85/mzID documentation built on May 31, 2019, 11:14 a.m.