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mzID (version 1.10.2)

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

Description

This class stores all parsed information from mzIdentML files

Usage

## S3 method for class 'mzID':
show(object)
## S3 method for class 'mzID':
length(x)
## S3 method for class 'mzID':
removeDecoy(object)
## S3 method for class 'mzID':
database(object, safeNames = TRUE)
## S3 method for class 'mzID':
evidence(object, safeNames = TRUE)
## S3 method for class 'mzID':
parameters(object)
## S3 method for class 'mzID':
software(object)
## S3 method for class 'mzID':
files(object)
## S3 method for class 'mzID':
peptides(object, safeNames = TRUE)
## S3 method for class 'mzID':
modifications(object)
## S3 method for class 'mzID':
id(object, safeNames = TRUE)
## S3 method for class 'mzID':
scans(object, safeNames = TRUE)
## S3 method for class 'mzID':
idScanMap(object)
## S3 method for class '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

Methods (by generic)

  • show: Short summary of object content
  • length: Get number of psm' in object
  • removeDecoy: Remove decoys from mzID object
  • database: Get the database used for searching
  • evidence: Get the evidence from the peptide search
  • 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
  • peptides: Get the peptides identified.
  • modifications: Get the modification on the identified peptides
  • id: Get the identification results
  • scans: Get the scans matched to peptides
  • idScanMap: Get the link between scans and identifications
  • c: Combine mzID and mzIDCollection objects

Objects from the class

Objects can be created using the mzID constructor, which handles parsing of mzIdentML files

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.

References

http://www.psidev.info/mzidentml

See Also

mzID

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