GenomicRegionsAnnotate: extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object

Description

extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object

Usage

# GenomicRegionsAnnotate(.Object1, .Object2,
# AnnotationsHeaders=NULL, sep.character="; ",
# complete.inclusion=FALSE, annotationAsRange=FALSE,
# getJustFeaturesNumber=FALSE)
GenomicRegionsAnnotate(.Object1, .Object2, ...)

Arguments

.Object1

An object of class GenomicRegions

.Object2

An object of class GenomicAnnotations

...

See below

AnnotationsHeaders:: Names of optional annotations fields from GenomicAnnotations object that are used to annotate the GenomicRegions object. Multiple annotation fields can be used
sep.character:: Character sequence used to separate annotation features
complete.inclusion:: Logical, if TRUE only annotations features entirely covered by one of the genomic regions are considered. (e.g. a gene completely included in the genomic regions from start to end) If FALSE also partial overlapping annotation features are used
annotationAsRange:: Logical, if TRUE only the first and last annotation features associated to each the genomic region are returned
getJustFeaturesNumber:: Logical, if TRUE only the numbers of annotation features overlapping the genomic regions are returned. If TRUE, only the first element specified with AnnotationsHeaders parameter is considered.

Value

A GenomicRegions object with optionalAnnotations

Details

The annotation features overlapping the input genomic regions are used to add optional annotations field to the GenomicRegions object.

If previous optional annotations fields are present, they are preserved as well in the output object