IdMapCounts {IdMappingAnalysis} | R Documentation

## The IdMapCounts class

### Description

Package: IdMappingAnalysis
Class IdMapCounts

`Object`
`~~|`
`~~+--``IdMapBase`
`~~~~~~~|`
`~~~~~~~+--``IdMapCounts`

Directly known subclasses:

public static class IdMapCounts
extends IdMapBase

An IdMapCounts object enapsulates a `data.frame` where the first column contains the primary ID set while the rest of columns contain the counts of secondary IDs for each Id Map in a given idMapList object, one column per ID Map, each ID Map related column having a name representing the given DB data source (i.e. 'NetAffx', 'EnVision' etc.) The constructor creates the IdMapCounts object from the list of ID Maps aligned by the primary IDs and primary and secondary keys. The easest way to obtain the list of properly aligned IdMap objects is to create a JointIdMap object from a set of un-aligned ID maps and then invoke the getIdMapList() method on this object. The IdMapCounts object can also be created directly from JointIdMap object by using the JointIdMap.$getCounts() method.

### Usage

    IdMapCounts(idMapList=NULL, verbose=FALSE, ...)

### Arguments

`idMapList` | The `list` of ID Maps aligned on primary IDs.
`verbose` | If `TRUE` enables diagnostic messages.Default is `FALSE`
`...` | Not used.

### Fields and Methods

Methods:

| `getStats` | Retrieves a set of unique counts of secondary IDs.
| `plot` | Compute and plot the (inversed) ecdf for each ID Map count entry within the IdMapCounts object.

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

     idMaps<-IdMap$as.list(examples$identDfList[[1]]);
     cnts<-IdMapCounts(IdMap(examples$identDfList[[1]]));
     cnts[1:20,];

     #create IdMapCounts object from aligned IdMap list.
     jointIdMap<-JointIdMap(examples$identDfList);
     idMaps<-jointIdMap$getIdMapList(verbose=TRUE);
     cnts<-IdMapCounts(idMaps);
     cnts[1:20,];

     #create IdMapCounts object directly from the JointIdMap object
     jointIdMap<-JointIdMap(examples$identDfList);
     cnts<-jointIdMap$getCounts(verbose=TRUE);

[Package IdMappingAnalysis version 1.24.0 Index]