IdMapDiffCounts {IdMappingAnalysis} | R Documentation

## The IdMapDiffCounts class

### Description

Package: IdMappingAnalysis
Class IdMapDiffCounts

`Object`
`~~|`
`~~+--``IdMapBase`
`~~~~~~~|`
`~~~~~~~+--``IdMapDiffCounts`

Directly known subclasses:

public static class IdMapDiffCounts
extends IdMapBase

The IdMapDiffCounts class handles statistics on IdMapDiff object. IdMapDiffCounts object encapsulates a data frame with row names corresponding to the primary IDs and 6 columns subdivided into pairs <match(TRUE/FALSE),count> each pair corresponding to the disjoint events <A-A*B,A*B,B-A*B>, where A and B are secondary ID lists for ID Maps A and B from the IdMapDiff object. The 'pairNames' attribute of the IdMapDiffCounts contains the names of the source ID Map pair from which the IdMapDiff object was created.

### Usage

    IdMapDiffCounts(idMapDiff=NULL, verbose=FALSE, ...)

### Arguments

`idMapDiff` | The IdMapDiff on which IdMapDiffCounts is cretated. Default is `NULL`.
`verbose` | If `TRUE` enables diagnostic messages. Default is `FALSE`.
`...` | Not used.

### Fields and Methods

Methods:

| `getCompoundEvents` | Get compound events.
| `getCompoundGroups` | Get counts for each compound event in IdMapDiffCounts.
| `plot` | Produce a fountain plot representing the quantitative relationship of the compound events.
| `summary` | Get a compaund event counts summary report.

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);

     #create IdMapDiff object
     diffs<-jointIdMap$getDiff("NetAffx_F","DAVID_Q",verbose=TRUE);

     # create IdMapDiffCounts object
     diffCounts<-IdMapDiffCounts(diffs);
     diffCounts[1:10,];

[Package IdMappingAnalysis version 1.28.0 Index]