GenomicRegionsAnnotate {PREDA} | R Documentation |
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.
|
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
Value
A GenomicRegions object with optionalAnnotations
[Package
PREDA version 1.36.0
Index]