mzIDpsm-class {mzID} | R Documentation |
This class handles parsing and storage of scan info and the related psm's. This information resides in the /*/x:DataCollection/x:AnalysisData/x:SpectrumIdentificationList/x:SpectrumIdentificationResult node.
## S4 method for signature 'mzIDpsm' show(object) ## S4 method for signature 'mzIDpsm' length(x) ## S4 method for signature 'mzIDpsm' id(object, safeNames = TRUE) ## S4 method for signature 'mzIDpsm' scans(object, safeNames = TRUE) ## S4 method for signature 'mzIDpsm' idScanMap(object)
object |
An mzIDpsm object |
x |
An mzIDpsm object |
safeNames |
Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files? |
The content of the class is stored as two data frames: One containing a row for each scan in the results, and one containing all psm's in the results. Additionally a list containing indexing from scan to psm is stored.
show
: A short summary of the content
length
: Get the number of psm'
id
: Get the identification results
scans
: Get the scans matched to peptides
idScanMap
: Get the link between scans and identifications
scans
A data.frame containing all reference to all scans with at least one psm. The columns gives at least an ID, a spectrumID and a reference to the file used.
id
A data.frame containing all psm's from the analysis. The columns depend on the file but at least id, chargeState, experimentalMassToCharge, passThreshold and rank must exist according to the mzIdentML specifications.
mapping
A list with an entry for each row in @scans. Each entry contains an integer vector pointing to the related rows in @id.
Objects of mzIDpsm are not meant to be created explicitly but as part of the
mzID-class
. Still object can be created with the constructor
mzIDpsm
.
Other mzID.classes: mzID-class
,
mzIDCollection-class
,
mzIDdatabase-class
,
mzIDevidence-class
,
mzIDparameters-class
,
mzIDpeptides-class