ChipDataSet is a S4 class to store input values, intermediate
calculations and results of ChIP-seq peaks analysis.
GRanges. ChIP-seq peaks.
GRanges. Genomic region(s) to extract peaks from.
Data.Frame. Genomic distribution of the peaks at distinct genomic features (TSSs, exons, introns, intergenic regions).
Data.Frame. Estimated characteristics (features) of the peaks.
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.
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