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