mzID (version 1.10.2)

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

Description

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

Usage

## S3 method for class 'mzIDdatabase':
show(object)
## S3 method for class 'mzIDdatabase':
length(x)
## S3 method for class '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?

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

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.

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).

See Also

mzIDdatabase

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