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
with the interaction information. More precisely, the
InteractionInfo object contains the following columns:
The p-value of the interaction.
The FDR of the interaction.
The order the interaction was entered into the model.
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
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
Ioannis Vardaxis, firstname.lastname@example.org
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.
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