IdMapDiff {IdMappingAnalysis} | R Documentation |
Package: IdMappingAnalysis
Class IdMapDiff
Object
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IdMapBase
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IdMapDiff
Directly known subclasses:
public static class IdMapDiff
extends IdMapBase
IdMapDiff constructor implements most time consuming step in comparing
two DBs and the structure itself stores the results in a compact form.
The IdMapDiff object encapsulates a data.frame
the first column
of which contains the primary IDs and the rest of columns contain a disjoint
representation of the ID Map pair in the form of 3 columns <A-A*B,A*B,B-A*B>,
where A and B are secondary ID lists for ID Maps A and B.
This class is separated from the IdMapDiffCounts
in anticipation of being used by various processing pipelines in a future.
IdMapDiff(idMap1=NULL, idMap2=NULL, pairNames=c("First", "Second"), verbose=FALSE, ...)
idMap1 |
The first ID Map object on which IdMapDiff object is constructed. |
idMap2 |
The second ID Map object on which IdMapDiff object is constructed. |
pairNames |
The character vector of length 2 representing the names of the ID Map pair. Default is c('First','Second'). |
verbose |
If |
... |
Not used. |
Methods:
No methods defined.
Methods inherited from IdMapBase:
[, aligned, as.data.frame, dim, dimnames, getName, primaryIDs, primaryKey, secondaryKey
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
Alex Lisovich, Roger Day
#get primary IDs from an msms experiment set IDs<-IdMapBase$primaryIDs(examples$msmsExperimentSet); #create JointIdMap object aligned by primaryIDs jointIdMap<-JointIdMap(examples$identDfList,primaryIDs=IDs); # get IdMap list aligned of two ID maps aligned by primaryIDs idMaps<-jointIdMap$getIdMapList(verbose=TRUE); #create IdMapDiff object diffs<-IdMapDiff(idMaps[["NetAffx_F"]],idMaps[["DAVID_Q"]]); diffs[1:10,]; # create IdMapDiff object directly from JointIdMap diffs<-jointIdMap$getDiff("NetAffx_F","DAVID_Q",verbose=TRUE);