addStrandCombination {sevenC} | R Documentation

## 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

`gi` | `GInteractions`
`colname` | name of the new column that is created in `gi`.

### 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"]
    )

[Package sevenC version 1.4.0 Index]