R: Add column to 'GInteractions' with overlap support.

addInteractionSupport {sevenC}

R Documentation

Add column to `GInteractions` with overlap support.

Description

See overlap methods in InteractionSet package for more details on the overlap calculations: ?overlapsAny

Usage

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")