reannotate: Transform an eSet object of Bioc-annotation into of...

In bedapub/ribiosExpression: Expression Analysis with RibiosExpression

Transform an eSet object of Bioc-annotation into of GTI-annotation

Description

The function is used to transform an eSet object, which is annotated by Bioconductor annotation packages, into an object with annotation information from GTI.

Usage

reannotate(object, check.target, ...)

Arguments

object	An eSet object, with the annotation slot set as one of the valid annotations recognized by Bioconductor, for instance hgu95av2.
check.target	Logical, with FALSE as default. When set to TRUE, beforing fetching database for annotations, the function first checks whether the chip type is supported by GTI. If it is not the case, the function will print error message and stop.
...	Currently not implemented

Details

The translation between Bioconductor annotation package names and GTI chip types is performed by the bioc2gti function in the ribiosAnnotation package.

Once the re-annotation succeeds, the annotation slot of the eSet object will be overwritten by the corresponding chip type name in GTI.

Value

An eSet object with feature annotations updated by GTI, and the annotation slot is changed to the chip type in GTI.

Author(s)

Jitao David Zhang <[e-mail]>

See Also

annotate to annotate an eSet object without prior information of bioc-annotation, or if that information is not saved in the annotation slot.

Examples

data(ribios.ExpressionSet)
print(ribios.ExpressionSet)

## Not run: 
gti.eSet <- reannotate(ribios.ExpressionSet)
gti.eSet <- reannotate(ribios.ExpressionSet, check.target=FALSE)
print(gti.eSet)

## End(Not run)

bedapub/ribiosExpression documentation built on Sept. 2, 2023, 4:37 a.m.