Class "AnnotationParams"

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Description

Class to store annotation parameters to automatically query a Biomart server, retrieve relevant annotation for a set of features of interest using, for example getGOFromFeatures and makeGoSet.

Objects from the Class

Objects can be created and set with the setAnnotationParams function. Object are created by calling without any arguments setAnnotationParams(), which will open an interactive interface. Depending on the value of "many.graphics" option, a graphical of a text-based menu will open (the text interface can be forced by setting the graphics argument to FALSE: setAnnotationParams(graphics = FALSE)). The menu will allow to select the species of interest first and the type of features (ENSEMBL gene identifier, Entrez id, ...) second.

The species that are available are those for which ENSEMBL data is available in Biomart and have a set of attributes of interest available. The compatible identifiers for downstream queries are then automatically filtered and displayed for user selection.

It is also possible to pass a parameter inputs, a character vector of length 2 containing a pattern uniquely matching the species of interest (in position 1) and a patterns uniquely matching the feature types (in position 2). If the matches are not unique, an error will be thrown.

A new instance of the AnnotationParams will be created to enable easy and automatic query of the Mart instance. The instance is invisibly returned and stored in a global variable in the pRoloc package's private environment for automatic retrieval. If a variable containing an AnnotationParams instance is already available, it can be set globally by passing it as argument to the setAnnotationParams function. Globally set AnnotationParams instances can be accessed with the getAnnotationParams function.

See the pRoloc-theta vignette for details.

Slots

mart:

Object of class "Mart" from the biomaRt package.

martname:

Object of class "character" with the name of the mart instance.

dataset:

Object of class "character" with the data set of the mart instance.

filter:

Object of class "character" with the filter to be used when querying the mart instance.

date:

Object of class "character" indicating when the current instance was created.

biomaRtVersion:

Object of class "character" with the biomaRt version used to create the AnnotationParams instance.

.__classVersion__:

Object of class "Versions" with the version of the AnnotationParams class of the current instance.

Methods

show

signature(object = "AnnotationParams"): to display objects.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

See Also

getGOFromFeatures, makeGoSet and the pRoloc-theta vignette.

Examples

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data(andy2011params)
andy2011params
data(dunkley2006params)
dunkley2006params

try(setAnnotationParams(inputs = c("nomatch1", "nomatch2")))
setAnnotationParams(inputs = c("Homo sapiens",
                        "UniProt/Swissprot Accession"))
getAnnotationParams()

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