GenomeMap-class {MACPET} | R Documentation

## GenomeMap S4 Class

### Description

`GenomeMap` class in a S4 class which inherits from the `GInteractions` class and it contains all the interactions found by MACPET at Stage 4. This class represents the genome map constructed by the peaks which interact. Furthermore, in the `metadata` field, it contains a `DataFrame` called `InteractionInfo` with the interaction information. More precisely, the `InteractionInfo` object contains the following columns:

`pvalue`

  The p-value of the interaction.

`FDR`

  The FDR of the interaction.

`Order`

  The order the interaction was entered into the model.

`TotalInterPETs`

  The total interaction PETs between every two interacting peaks.

Finally it also contains two metadata columns with the peak summits of the two peaks in each interaction.

### Details

`GenomeMap` class is created by the `MACPETUlt` function at Stage 4. Interactions with same `Order` are those who entered the model together because they had the same `FDR` value. Subsets of significant interactions can be found using the `GetSignInteractions` function.

### Author(s)

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

### References

Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.

### See Also

`plot`, `summary`,`GetSignInteractions`, `MACPETUlt`, `GetShortestPath`

[Package MACPET version 1.14.0 Index]