annotateTranscripts: annotateTranscripts

Description

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

Usage

annotateTranscripts(object, annot, min.overlap = 0.3)
## S3 method for class '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.

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.

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.

Examples

Run this code

### 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)