getQuadProb-methods: getQuadProb

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

Description

Retrieve all internal calculations performed by predictStrand function.

Usage

getQuadProb(object, strand)

## S4 method for signature 'ChipDataSet'
getQuadProb(object, strand)

Arguments

object	A ChipDataSet object.
strand	Character. The strand to extract calculations for. One of ["+", "-"].

Value

A nine column Data.Frame, where each row corresponds to a ChIP-seq peak and each column keeps one of the intermediate calculations:

• max.cov - maximum coverage of the RNA-seq fragments inside the peak region.

• pass.cov.treshold - whether the max.cov exceeds the coverage.cutoff, either user defined or estimated from RNA-seq data by estimateBackground function call and stored in TranscriptionDataSet object.

• q1q2.sepline.coord - genomic coordinate corresponding to the transcription start position inside the peak region.

• q1.coord - genomic coordinates of q1.

• q2.coord - genomic coordinates of q2.

• q1.count - total number of fragments in q1.

• q2.count - total number of fragments in q2.

• q1.prob - probability of a fragment being sampled from the q1.

• q2.prob - probability of a fragment being sampled from the q2.

Author(s)

Armen R. Karapetyan

See Also

predictStrand

Examples

### Load ChipDataSet object
data(cds)

### Load TranscriptionDataSet object
data(tds)

head(getQuadProb(cds, strand = "+"))
head(getQuadProb(cds, strand = "-"))

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