mzID (version 1.10.2)

mzIDparameters-class: A Class to store analysis information from the mzIdentML file

Description

This class tries to collect the multitude of different analysis information required to rerun the analysis. The intended data to be stored are: The software used in the analysis of the data, the location and nature of the rawfile(s), the location and nature of the database file(s), the location of the mzIDentML file itself as well as all the parameters used during the analysis leading to the mzIdentML file. Information regarding how the LC-MS experiment was performed should be collected from the raw data file. As the parameters used in different software solutions can vary greatly, all these parameters are stored in a named list, which can thus be very different from pipeline to pipeline. It is the users responsibility to check conformity between samples.

Usage

## S3 method for class 'mzIDparameters':
show(object)
## S3 method for class 'mzIDparameters':
length(x)
## S3 method for class 'mzIDparameters':
parameters(object)
## S3 method for class 'mzIDparameters':
software(object)
## S3 method for class 'mzIDparameters':
files(object)

Arguments

object

An mzIDparameters object

x

An mzIDparameters object

Methods (by generic)

• show: Short summary of the content
• length: Get the length of the object
• 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

Objects from the class

Objects of mzIDparameters are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDparameters (not exported).

See Also

mzIDparameters

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