GenomicAnnotationsExtract: extract optional annotations for a specific region
In PREDA: Position Related Data Analysis

Description Usage Arguments Details Value See Also

extract optional annotations for a specific region

# GenomicAnnotationsExtract(.Object, chr, start, end,
# AnnotationsHeader=NULL, sep.character="; ",
# complete.inclusion=FALSE, skipSorting=FALSE,
# annotationAsRange=FALSE, getJustFeaturesNumber=FALSE)

GenomicAnnotationsExtract(.Object, ...)

.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

Extract annotations associated to a specific genomic region from a GenomiAnnotations object. Only annotations from the specified columns are returned.

A character vector is returned

"GenomicAnnotations"

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