mzID-class: A class to contain data from mzIdentML-files

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

Description

This class stores all parsed information from mzIdentML files

Usage

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## 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)

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

References

http://www.psidev.info/mzidentml

See Also

mzID

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


mzID documentation built on Nov. 8, 2020, 8:08 p.m.