GenomeMap-class: GenomeMap S4 Class

Description Details Author(s) References See Also

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, Drabl<c3><b8>s F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.

See Also

plot, summary,GetSignInteractions, MACPETUlt, GetShortestPath


MACPET documentation built on Nov. 8, 2020, 5:47 p.m.