IdMappingRetrieval (version 1.20.0)

getIdMapList.ServiceManager: Collect ID mapping data from various online query systems utilizing Annotation service functionality

Description

Collect ID mapping data from various online query systems utilizing Annotation service functionality. If called as static i.e. ServiceManager$getIdMapList(...), a set of default services will be used to collect data from.

Usage

"getIdMapList"(this, arrayType="menu", selection="menu", primaryKey="From", secondaryKey="To", force=FALSE, graphics=TRUE, verbose=FALSE, ...)

Arguments

arrayType

The Affymertix microarray name. If 'menu', display a set of all available array types, allowing user to select one. If arrayType is an array name, the function performs the name correctness check. Default is 'menu'.

selection

The character vector of service names which data are to be retrieved. If "menu" displays the available choices according to the names of services encapsulated within the ServiceManager object. Default is 'menu'.

primaryKey

The name which will be assigned to each resulting IdMap object primary column at the end of a data retrieval process. Default is 'From'.

secondaryKey

The name which will be assigned to each resulting IdMap object secondary column at the end of a data retrieval process. Default is 'To'.

force

If TRUE forces the system to update the content of service data directory even if contained the data before.

graphics

If TRUE and selection='menu', the attempt to will be made to use graphical capabilities of the rChoiceDialogs package to select a subset of services to collect data from.

verbose

if TRUE enables diagnostic messages.

...

Not used.

Value

See Also

For more information see ServiceManager.

Examples

 ## Not run: 
#    Annotation$init();
#    AnnotationAffx$setCredentials(user="[e-mail]",password="125438",verbose);
#    #create service manage object encapsulating default services
#    svm<-ServiceManager(ServiceManager$getDefaultServices());
#    #retrieve the ID Map list interactively selecting array type and services
#    idMapList<-getIdMapList(svm,arrayType="menu",selection="menu",verbose=TRUE);
#    # use a static call to collect data using default services
#    idMapList<-ServiceManager$getIdMapList(arrayType="menu",selection="menu",verbose=TRUE);
#  ## End(Not run)