getQuadProb {transcriptR} | R Documentation

## getQuadProb

### 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 = "-"))

[Package transcriptR version 1.12.0 Index]