mzIDpsm-class: A class to store psm information from an mzIdentML file

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

Description

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.

Usage

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## 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)

Arguments

object

An mzIDpsm object

x

An mzIDpsm 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 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.

Methods (by generic)

Slots

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 from the class

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.

See Also

mzIDpsm

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


mzID documentation built on May 31, 2017, 11:05 a.m.