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