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, DrablĂ¸s F, Rye M and Lindqvist BH (2018). *MACPET: Complete pipeline for ChIA-PET*.
To be published.

`plot`

,
`summary`

,`GetSignInteractions`

,
`MACPETUlt`

, `GetShortestPath`

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.