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

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

## S3 method for class 'mzIDpsm':
show(object)
## S3 method for class 'mzIDpsm':
length(x)
## S3 method for class 'mzIDpsm':
id(object, safeNames = TRUE)
## S3 method for class 'mzIDpsm':
scans(object, safeNames = TRUE)
## S3 method for class 'mzIDpsm':
idScanMap(object)

Arguments

object

An mzIDpsm object

safeNames

Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Methods (by generic)

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

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.

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.