importAnnotationExternal {TSRchitect} | R Documentation

## importAnnotationExternal

### Description

`importAnnotationExternal` imports an annotation from an external file and attaches it to the tssObject

### Usage

    importAnnotationExternal(experimentName, fileType, annotFile)

      ## S4 method for signature 'tssObject,character,character'
    importAnnotationExternal(experimentName,
      fileType = c("bed", "gff", "gff3"), annotFile)

### Arguments

`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.

### Value

fills the slot @annotation in the returned tssObject with a GRanges object contining a parsed annotation file of the selected type.

### Note

`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`.

### Examples

    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)

[Package TSRchitect version 1.8.9 Index]