IdMapDiff {IdMappingAnalysis} | R Documentation

## The IdMapDiff class

### Description

Package: IdMappingAnalysis
Class IdMapDiff

`Object`
`~~|`
`~~+--``IdMapBase`
`~~~~~~~|`
`~~~~~~~+--``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.

### Usage

    IdMapDiff(idMap1=NULL, idMap2=NULL, pairNames=c("First", "Second"), verbose=FALSE, ...)

### Arguments

`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 `TRUE` enables diagnostic messages.
`...` | Not used.

### Fields and Methods

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

### Author(s)

Alex Lisovich, Roger Day

### Examples

     #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);

[Package IdMappingAnalysis version 1.28.0 Index]