ChipDataSet-class {transcriptR} | R Documentation

## 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`

[Package transcriptR version 1.12.0 Index]