getTranscripts-methods: getTranscripts

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

Description

Retrieve transcripts information from the TranscriptionDataSet object.

Usage

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

### Load TranscriptionDataSet object
data(tds)

### View detected transcripts
getTranscripts(tds)

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