This class stores all parsed information from mzIdentML files
Usage
## S4 method for signature 'mzID'
show(object)
## S4 method for signature 'mzID'
length(x)
## S4 method for signature 'mzID'
removeDecoy(object)
## S4 method for signature 'mzID'
database(object, safeNames = TRUE)
## S4 method for signature 'mzID'
evidence(object, safeNames = TRUE)
## S4 method for signature 'mzID'
parameters(object)
## S4 method for signature 'mzID'
software(object)
## S4 method for signature 'mzID'
files(object)
## S4 method for signature 'mzID'
peptides(object, safeNames = TRUE)
## S4 method for signature 'mzID'
modifications(object)
## S4 method for signature 'mzID'
id(object, safeNames = TRUE)
## S4 method for signature 'mzID'
scans(object, safeNames = TRUE)
## S4 method for signature 'mzID'
idScanMap(object)
## S4 method for signature 'mzID'
c(x, y, ..., recursive = FALSE)
Arguments
object
An mzID object
x
An mzID object
safeNames
Should column names be lowercased to ensure compatibility
between v1.0 and v1.1 files?
y
An mzID or mzIDCollection object
...
ignored
recursive
ignored
Details
The mzID class stores information in a subset of classes, each class having
its own slot. While these classes should not need to be accessed directly,
descriptions of their content is delegated to each respective class.
Methods (by generic)
show: Short summary of object content
length: Get number of psm' in object
removeDecoy: Remove decoys from mzID object
database: Get the database used for searching
evidence: Get the evidence from the peptide search
parameters: Get the parameters used for the search
software: Get the software used to arrive at the results
files: Get the data files used for the analysis
peptides: Get the peptides identified.
modifications: Get the modification on the identified peptides
id: Get the identification results
scans: Get the scans matched to peptides
idScanMap: Get the link between scans and identifications
c: Combine mzID and mzIDCollection objects
Slots
parameters
An instance of mzIDparameters-class. This
object contains all information related to how the analysis was carried out.
psm
An instance of mzIDpsm-class. This object contains
the meat of the analysis with all scans and their related PSMs recorded.
peptides
An instance of mzIDpeptides-class. This object
contains a library of all peptides generated from the database along with
possible modifications.
evidence
An instance of mzIDevidence-class. This object
lists all peptides detected in the analysis with reference to the
mzIDpeptides instance.
database
An instance of mzIDdatabase-class. This object
contains information on the proteins in the database. As the full database is
not recorded in mzIdentML files the actual protein sequence is not recorded
but there is sufficient information to retrieve it from the database file.
Objects from the class
Objects can be created using the mzID constructor, which
handles parsing of mzIdentML files