Description Usage Arguments Details Value Author(s) See Also Examples

Compute the distance between interacting regions on the linear genome, for each pairwise interaction contained in a GInteractions or InteractionSet object.

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`x` |
A GInteractions or InteractionSet object. |

`type` |
A character string specifying the type of distance to compute.
Can take values of |

For each interaction in `x`

, the `pairdist`

method computes the distance between the two interacting regions.
An integer vector is returned, with values computed according to the specified value of `type`

:

`"mid"`

:-
The distance between the midpoints of the two regions (rounded down to the nearest integer) is returned.

`"gap"`

:-
The length of the gap between the closest points of the two regions is computed - negative lengths are returned for overlapping regions, indicating the length of the overlap.

`"span"`

:-
The distance between the furthermost points of the two regions is computed.

`"diag"`

:-
The difference between the anchor indices is returned. This corresponds to a diagonal on the interaction space when bins are used in the

`regions`

slot of`x`

.

Interchromosomal interactions are marked with `NA`

.
Alternatively, if `type="intra"`

, a logical vector is returned indicating whether the interaction occurs between two regions on the same chromosome.
`intrachr(x)`

is an alias for `pairdist(x, type="intra")`

.

The return values of the assorted methods are the same for both GInteractions and InteractionSet objects.
Methods for the latter operate on the GInteractions object in the `interactions`

slot.

An integer or logical vector of distances.

Aaron Lun

`GInteractions-class`

,
`InteractionSet-class`

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