R: Get an IdMap object using the data retrieved by a particular...

getIdMap.Annotation {IdMappingRetrieval}

R Documentation

Get an IdMap object using the data retrieved by a particular service represented by annotation object

Description

Get an IdMap object using the data retrieved by a particular service represented by annotation object.

Usage

## S3 method for class 'Annotation'
getIdMap(this, arrayType="menu", primaryKey=NULL, secondaryKey=NULL, force=FALSE, graphics=TRUE, verbose=FALSE, ...)

Arguments

`arrayType`	A `character` string representing the array name. If 'menu', the list of available arrays is displayed allowing to select the array type of interest.
`primaryKey`	The name which will be assigned to the IdMap object primary column at the end of a data retrieval process.
`secondaryKey`	The name which will be assigned to the IdMap object secondary column at the end of a data retrieval process.
`force`	If `TRUE` forces the system to update the content of service data directory even if contained the data before. Used to update the annotation data if necessary. Default is `FALSE`.
`graphics`	If `TRUE` (default), the attempt to will be made to use graphical capabilities of the rChoiceDialogs package to display selection choices (items, files etc.) in a graphical form.
`verbose`	if `TRUE` enables diagnostic messages. Default is `FALSE`.
`...`	Additional parameters.

Value

An ID Map object

Author(s)

Alex Lisovich, Roger Day

Examples

## Not run: 
  Annotation$init();
  Annotation$setCredentials("Affymetrix",user="alex.lisovich@gmail.com",password="125438",verbose);
  #create Affymetrix annotation object
  annObj=AnnotationAffx();
  #retrieve the ID Map
  idMap<-getIdMap(annObj,arrayType="HG-U133_Plus_2",primaryKey="Affy",secondaryKey="Uniprot",verbose=TRUE);

## End(Not run)

[Package IdMappingRetrieval version 1.30.0 Index]