ChipDataSet-class {transcriptR} | R Documentation |
The ChipDataSet
is a S4 class to store input values, intermediate
calculations and results of ChIP-seq peaks analysis.
peaks
GRanges
. ChIP-seq peaks.
region
GRanges
. Genomic region(s) to extract peaks from.
genomicAnnotation
Data.Frame
. Genomic distribution of the peaks
at distinct genomic features (TSSs, exons, introns, intergenic regions).
features
Data.Frame
. Estimated characteristics (features) of the
peaks.
tssOverlapPrediction
List
. Prediction of the gene associated
peaks. The following elements are reported:
'predicted.tssOverlap' - predicted class (yes - gene associated; no - background) and probability of a ChIP-seq peak being classified as gene associated.
'confusionMatrix' - cross-tabulation of observed and predicted classes with associated statistics.
'logFitSummary' - statistical significance of the predictors used in the logistic regression.
'roc' - results of the receiver operating characteristic analysis.
strandPrediction
List
. Prediction of the peak strandedness. The
following elements are reported:
'predicted.strand' - predicted ChIP-seq peak strand.
'probability.cutoff' - probability cutoff for q2.
'results.plus' - intermediate calculations for the forward DNA strand.
'results.minus' - intermediate calculations for the reverse DNA strand.
Armen R. Karapetyan
constructCDS
predictTssOverlap
predictStrand