annotateTranscripts {transcriptR} | R Documentation

## annotateTranscripts

### Description

Annotate detected transcripts by the available reference annotations based on genomic overlap.

### Usage

    annotateTranscripts(object, annot, min.overlap = 0.3)

    ## S4 method for signature 'TranscriptionDataSet,GRanges'
    annotateTranscripts(object, annot,
      min.overlap = 0.3)

### Arguments

`object` | A `TranscriptionDataSet` object.
`annot` | `GRanges`. Reference annotations.
`min.overlap` | `Numeric`. A minimal proportion of the overlap between transcript and annotation. A value in the range (0, 1]. Default: 0.3.

### Details

Genomic overlap between transcript and annotation is calculated as the mean of two proportions: 1) proportion of the transcript length overlapping annotation; 2) proportion of the annotation length overlapping transcript. This approach levels off differences in length between transcript and annotation and, thus better suitable for cases in which the length of either transcript or annotation is much longer than of compared element.

If there is an overlap between transcript and annotation, the ID of the associated annotation will be linked to the transcript.

### Value

An extra column `annotation.overlap` will be added to the metadata portion of the `GRanges` object which is stored in the `transcripts` slot of the provided `TranscriptionDataSet` object.

### Author(s)

Armen R. Karapetyan

### See Also

`detectTranscripts`

### Examples

    ### Load TranscriptionDataSet object
    data(tds)

    ### Load reference annotations (knownGene from UCSC)
    data(annot)

    ### Detect transcripts
    detectTranscripts(object = tds, coverage.cutoff = 5, gap.dist = 4000,
    estimate.params = TRUE, combine.by.annot = FALSE, annot = annot)

    ### Annotate detected transcripts
    annotateTranscripts(object = tds, annot = annot)

    ### View detected transcripts and associated annotations
    getTranscripts(tds)

[Package transcriptR version 1.12.0 Index]