getQuadProb {transcriptR} | R Documentation |
Retrieve all internal calculations performed by predictStrand
function.
getQuadProb(object, strand) ## S4 method for signature 'ChipDataSet' getQuadProb(object, strand)
object |
A |
strand |
|
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.
Armen R. Karapetyan
### Load ChipDataSet object data(cds) ### Load TranscriptionDataSet object data(tds) head(getQuadProb(cds, strand = "+")) head(getQuadProb(cds, strand = "-"))