importAnnotationExternal {TSRchitect} | R Documentation |
importAnnotationExternal
imports an
annotation from an external file and attaches it to the
tssObject
importAnnotationExternal(experimentName, fileType, annotFile) ## S4 method for signature 'tssObject,character,character' importAnnotationExternal( experimentName, fileType = c("bed", "gff", "gff3"), annotFile )
experimentName |
- an S4 object of class tssObject that contains information about the experiment |
fileType |
- the format of the annotation file to be imported. Must be one of: "bed", "gff" or "gff3". |
annotFile |
- a path (full or relative) to the annotation file to be imported. |
fills the slot @annotation in the returned tssObject with a GRanges object contining a parsed annotation file of the selected type.
importAnnotationExternal
makes use of three functions from the
rtracklayer package:
import.bed
,
import.gff
, and
import.gff3
.
An example similar to the one provided can be found in
Example 2 from the vignette
(run TSRchitectUsersGuide()
to view the documentation).
To import directly from the AnnotationHub client, please
refer to
importAnnotationHub
.
load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect")) extdata.dir <- system.file("extdata", package="TSRchitect") annotation <- dir(extdata.dir, pattern="\\.gff3$", full.names=TRUE) tssObjectExample <- importAnnotationExternal(experimentName=tssObjectExample, fileType="gff3", annotFile=annotation)