An mzIdentML parser for R

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Documentation for package ‘mzID’ version 1.2.1

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mzID-package A parser for the mzIdentML file format
attrExtract Extract and properly format node attributes
attrExtractNameValuePair Extract and format attributes from nodes with name and value attributes
c-method Utility functions for mzIDCollection object
countChildren Report the number of children with specific name per node in an XML document
flatten Flatten an mzID related class into a table
flatten-method Flatten an mzID related class into a table
getAdditionalPar Extracts the additional, often software specific parameters
getDatabaseFile Retrive information on the database used in the analysis
getDatabaseFilter Looks for any database filters applied during the peptide search
getDatabaseTranslation Looks whether a translation table is present in the mzIdentML file and reports it if found
getEnzymes Extracts the enzymes used for digestion specified as specified in the software analysis
getFragmentTolerance Looks for presence of fragment tolerance settings and reports these if found
getMassTable Search for the presence of a mass table used during the search
getModifications Looks for presence of amino acid modification settings and reports these if found
getParentTolerance Looks for presence of parent tolerance settings and reports these if found
getPath Get the correct namespace path depending on version
getRawFile Retrive information on the raw files used in the analysis
getSearchType Gets the search type as specified in the mzIdentML file
getSoftware Retrive information on the software used in the analysis
getThreshold Finds the psm threshold used in the file
getVersion Get the mzIdentML version and check that the version is supported
isRemote Test whether a given string is a remote resource
length Report the length of an mzIDpsm object
length-method Report the length of an mzID object
length-method Get the length of an mzIDCollection object
length-method Report the length of an mzIDdatabase object
length-method Report the length of an mzIDevidence object
length-method Report the length of an mzIDparameters object
length-method Report the length of an mzIDpeptides object
length-method Report the length of an mzIDpsm object
length-method Report the length of an mzIDpsm object
mzID Parse an mzIdentML file
mzID-class A class to contain data from mzIdentML-files
mzIDCollection Create a new mzIDCollection
mzIDCollection-class A class to handle a set of mzID objects
mzIDdatabase A constructor for the mzIDdatabase class
mzIDdatabase-class A class to store database information from an mzIdentML file
mzIDevidence A constructor for the mzIDevidence class
mzIDevidence-class A class to store peptide evidence information from an mzIdentML file
mzIDparameters A constructor for the mzIDparameters class
mzIDparameters-class A class to store database information from an mzIdentML file
mzIDpeptides A constructor for the mzIDpeptides class
mzIDpeptides-class A class to store peptide information from an mzIdentML file
mzIDpsm A constructor for the mzIDpsm class
mzIDpsm-class A class to store psm information from an mzIdentML file
prepareXML Parses an xml file and defines the namespace
show Show method for mzIDpsm objects
show-method Show method for mzID objects
show-method Show method for mzIDCollection objects
show-method Show method for mzIDdatabase objects
show-method Show method for mzIDevidence objects
show-method Show method for mzIDparameters objects
show-method Show method for mzIDpeptides objects
show-method Show method for mzIDpsm objects
type.convert An extension of type.convert() to handle XML like logicals (lower case)
Utilities Utility functions for mzIDCollection object
[[-method Utility functions for mzIDCollection object