TranscriptionDataSet-class {transcriptR} | R Documentation

## TranscriptionDataSet

### Description

The `TranscriptionDataSet` is a S4 class to store input values, intermediate calculations and results of the transcripts detection and quantification analysis.

### Slots

`bamFile`

  `Character`. Path to a BAM file.

`fragments`

  `GRanges`. Sequencing reads extended to the fragment size.

`fragmentSize`

  `Numeric`. Fragment size in base pairs (bp).

`region`

  `GRanges`. Genomic region(s) to extract reads from.

`coveragePlus`

  `RleList`. Fragment coverage profile for the forward DNA strand.

`coverageMinus`

  `RleList`. Fragment coverage profile for the reverse DNA strand.

`coverageCutoff`

  `Numeric`. Background coverage cutoff value.

`coverageCutoffFdr`

  `Numeric`. False Discovery Rate (FDR) used to estimate background coverage cutoff.

`gapDistanceTest`

  `Data.Frame`. Tested gap distances and corresponding error rates.

`gapDistanceTestCovCutoff`

  `Numeric`. Coverage cutoff value used for the gap distance estimation.

`transcripts`

  `GRanges`. Identified transcripts.

`transcriptsCovCutoff`

  `Numeric`. Coverage cutoff value used for the transcripts detection.

`transcriptsGapDist`

  `Numeric`. Gap distance value used for the transcripts detection.

`transcriptsNormalization`

  `Numeric`. Total number of reads used for normalization when calculating FPKM.

### Author(s)

Armen R. Karapetyan

### See Also

`constructTDS`

[Package transcriptR version 1.12.0 Index]