annotateTranscripts-methods: annotateTranscripts

In transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

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)

transcriptR documentation built on Nov. 8, 2020, 8:12 p.m.