Add column to GInteractions with overlap support.

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")