getTranscripts-methods: getTranscripts

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Retrieve transcripts information from the TranscriptionDataSet object.

Usage

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getTranscripts(object, min.length, min.fpkm, min.coverage)

## S4 method for signature 'TranscriptionDataSet'
getTranscripts(object, min.length, min.fpkm,
  min.coverage)

Arguments

object

A TranscriptionDataSet object.

min.length

Numeric. A minimum length (in bp) of the reported transcripts.

min.fpkm

Numeric. A minimum FPKM of the reported transcripts.

min.coverage

Numeric. A minimum coverage of the reported transcripts.

Details

The coverage is a measure of how densely the transcript is covered by the sequencing fragments. Modestly/highly expressed transcripts will have a value close to 1, whereas lowly expressed transcripts will have a value close to 0, indicating the sparse distribution of sequencing fragments along the transcript body.

Value

A GRanges object.

Author(s)

Armen R. Karapetyan

See Also

detectTranscripts

Examples

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### Load TranscriptionDataSet object
data(tds)

### View detected transcripts
getTranscripts(tds)


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