getQuadProb-methods: getQuadProb

Description Usage Arguments Value Author(s) See Also Examples

Description

Retrieve all internal calculations performed by predictStrand function.

Usage

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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

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### Load ChipDataSet object
data(cds)

### Load TranscriptionDataSet object
data(tds)

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


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