TranscriptionDataSet-class: TranscriptionDataSet

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

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

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