GenomicAnnotationsFromLibrary: Function extracting a GenomicAnnotations object from a...

In PREDA: Position Related Data Analysis

Description

Function extracting a GenomicAnnotations object from a Bioconductor annotation library

Usage

GenomicAnnotationsFromLibrary(annotLibrary, probeIDs = NULL,
retain.chrs = NULL, optionalAnnotations = NULL)

Arguments

annotLibrary	Character string containing the name of the annotations library to be used for building the GenomicAnnotations object
probeIDs	Optional: list of reference id from the selected annotLibrary to be used for building the GenomicAnnotations object
retain.chrs	Numeric vector, containing the list of chromosomes selected for the output GenomicAnnotations object. E.g. set retain.chrs=1:22 to limit the GenomicAnnotations object to chromosomes from 1 to 22. This might be ueseful to limit GenomiAnnotations objects to autosomic chromosomes.
optionalAnnotations	Character vector to select additional annotations fields to be included into the GenomicAnnotations object.

Value

An object of class "GenomicAnnotations"

Author(s)

Francesco Ferrari

See Also

"GenomicAnnotations"

Examples

## Not run: 

GEGenomicAnnotations<-GenomicAnnotationsFromLibrary(annotLibrary=
"org.Hs.eg.db", retain.chrs=1:22)

# with optional annotations Genesymbols and EntrezGeneIDs
GEGenomicAnnotations<-GenomicAnnotationsFromLibrary(annotLibrary=
"hgu133plus2.db", retain.chrs=1:22,
optionalAnnotations=c("SYMBOL", "ENTREZID"))



## End(Not run)

PREDA documentation built on Nov. 8, 2020, 7:40 p.m.