mzIDdatabase-class: A class to store database information from an mzIdentML file
In mzID: An mzIdentML parser for R

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

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

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

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

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

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

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).

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

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

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.

mzIDdatabase

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