GenomicAnnotationsExtract {PREDA} | R Documentation |
extract optional annotations for a specific region
Description
extract optional annotations for a specific region
Usage
# GenomicAnnotationsExtract(.Object, chr, start, end,
# AnnotationsHeader=NULL, sep.character="; ",
# complete.inclusion=FALSE, skipSorting=FALSE,
# annotationAsRange=FALSE, getJustFeaturesNumber=FALSE)
GenomicAnnotationsExtract(.Object, ...)
Arguments
.Object |
An object of class GenomicAnnotations
|
... |
See below
- chr:
-
Coordinate for the selected genomic region
- start:
-
Coordinate for the selected genomic region
- end:
-
Coordinate for the selected genomic region
- AnnotationsHeader:
-
Character or numeric vector to select the annotations columns
to be considered
- sep.character:
-
Character used to separate annotated features in the ouptput
- complete.inclusion:
-
Logical, if TRUE only annotated features completely included
in the region are reported. If FALSE (default), every overlapping
the feature is considered.
- skipSorting:
-
Logical, if TRUE, annotation sorting is skipped before
processing output (to save computational time, e.g. in a long loop)
- annotationAsRange:
-
If TRUE, then only the first and last annotated element in
the region are reported
- getJustFeaturesNumber:
-
Logical: if TRUE, just the number of annotated features in
the region is returned
|
Details
Extract annotations associated to a specific genomic region
from a GenomiAnnotations object. Only annotations from the
specified columns are returned.
Value
A character vector is returned
See Also
"GenomicAnnotations"
[Package
PREDA version 1.36.0
Index]