GenomeMap-class: GenomeMap S4 Class
In IoannisVardaxis/MACPET: Model based analysis for paired-end data

Description Details Author(s) References See Also

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.

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.

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

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

plot, summary,GetSignInteractions, MACPETUlt, GetShortestPath