getAnnotation: Retrieves annotations for an "ExpressionSet"

In jotsetung/unsoRted: Unsorted R functions and utilities

Description

Function to retrieve annotations for probe sets of a given “ExpressionSet” object from anntation package provided by Bioconductor.

Usage

getAnnotation( x, ann.source="bioconductor", what=c( "accnum", "symbol",
"entrezid", "chr", "ensembl" ) )
getAnnotationForIDs( x, chip, ann.source="bioconductor", what=c( "accnum", "symbol",
"entrezid", "chr", "ensembl" ) )

Arguments

x	An “ExpressionSet” object for which the annotations should be returned (for function getAnntotation), or character vector of probe set ids (for function getAnnotationForIDs).
chip	The type of microarray for which the annotation should be returned.
ann.source	Currently not used; should enable to switch from annotations provided form Bioconductor to e.g. Biomart based annotations.
what	The character that can/will be used to split the elements.

Details

The function might get improved in future as, at present, it is pretty slow.

Value

A data.frame (same ordering as the probe set ids in featureNames of the ExpressionSet with annotations retrieved for the probe set ids.)

Author(s)

Johannes Rainer

References

http://bioinfo.i-med.ac.at

jotsetung/unsoRted documentation built on May 19, 2019, 9:42 p.m.