Add combination of anchor strand orientation.

Description

Each anchor region has a strand that is '+' or '-'. Therefore, the each interaction between two regions has one of the following strand combinations: "forward", "reverse", "convergent", or "divergent". Unstranded ranges, indicated by *, are treated as positive strand.

Usage

addStrandCombination(gi, colname = "strandOrientation")

Arguments

Value

The same GInteractions as gi but with an additional column indicating the four possible combinations of strands "forward", "reverse", "convergent", or "divergent".

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"
)

# add combination of anchor strands as new metadata column
gi <- addStrandCombination(gi)

# build small matrix to check strand combination
cbind(
as.character(strand(anchors(gi, "first"))),
as.character(strand(anchors(gi, "second"))),
mcols(gi)[, "strandOrientation"]
)