Add column to GInteractions with overlap support. — addInteractionSupport (original) (raw)
See overlap methods in InteractionSet package for more details on the overlap calculations: ?overlapsAny
addInteractionSupport(gi, subject, colname = "loop", ...)
Arguments
| gi | GInteractions object |
|---|---|
| subject | another GInteractions object |
| colname | name of the new annotation column in gi. |
| ... | additional arguments passed to overlapsAny. |
Value
InteractionSet gi as input but with additional annotation column colname indicating whether each interaction is supported by subject or not.
Examples
build example GRanges as anchors
anchorGR <- GRanges( rep("chr1", 4), IRanges( c(1, 5, 20, 14), c(4, 8, 23, 17) ), strand = c("+", "+", "+", "-"), score = c(5, 4, 6, 7) )
build example GIntreaction object
gi <- GInteractions( c(1, 2, 2), c(4, 3, 4), anchorGR, mode = "strict" )
build exapple support GInteractions object
exampleSupport <- GInteractions( GRanges("chr1", IRanges(1, 4)), GRanges("chr1", IRanges(15, 20)) )
add support
gi <- addInteractionSupport(gi, subject = exampleSupport)
Use colname argument to add support to differnt metadata column name
gi <- addInteractionSupport(gi, subject = exampleSupport, colname = "example")