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 |