ChipDataSet

Description

The ChipDataSet is a S4 class to store input values, intermediate calculations and results of ChIP-seq peaks analysis.

Slots

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.

Author(s)

Armen R. Karapetyan

See Also

constructCDS predictTssOverlap predictStrand