PREDA (version 1.18.0)

GenomicAnnotationsExtract: 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

Value

A character vector is returned

Details

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

See Also

"GenomicAnnotations"