Annotate detected transcripts by the available reference annotations based on genomic overlap.
1 2 3 4 5
annotateTranscripts(object, annot, min.overlap = 0.3) ## S4 method for signature 'TranscriptionDataSet,GRanges' annotateTranscripts(object, annot, min.overlap = 0.3)
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.
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
Armen R. Karapetyan
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
### 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)