anchor {plyranges} | R Documentation

## Anchored Ranges objects

### Description

The `GRangesAnchored` class and the `IRangesAnchored` class allow components of a `GRanges` or `IRanges` (start, end, center) to be held fixed.

### Usage

    anchor(x)

    unanchor(x)

    anchor_start(x)

    anchor_end(x)

    anchor_center(x)

    anchor_centre(x)

    anchor_3p(x)

    anchor_5p(x)

### Arguments

`x` | a Ranges object

### Details

Anchoring will fix a Ranges start, end, or center positions, so these positions will remain the same when performing arithimetic. For `GRanges` objects, the function (`anchor_3p()`) will fix the start for the negative strand, while `anchor_5p()` will fix the end for the positive strand. Anchoring modifies how arithmetic is performed, for example modifying the width of a range with `set_width()` or stretching a range with `stretch()`. To remove anchoring use `unanchor()`.

### Value

a RangesAnchored object which has the same appearance as a regular Ranges object but with an additional slot displaying an anchor.

### Constructors

Depending on how you want to fix the components of a Ranges, there are five ways to construct a RangesAnchored class. Here `x` is either an `IRanges` or `GRanges` object.

- `anchor_start(x)`Fix the start coordinates

- `anchor_end(x)`Fix the end coordinates

- `anchor_center(x)`Fix the center coordinates

- `anchor_3p(x)`On the negative strand fix the start coordinates, and for positive or unstranded ranges fix the end coordinates.

- `anchor_5p(x)`On the positive or unstranded ranges fix the start coordinates, coordinates and for negative stranded ranges fix the end coordinates.

### Accessors

To see what has been anchored use the function `anchor`. This will return a character vector containing a valid anchor. It will be set to one of `c("start", "end", "center")` for an `IRanges` object or one of `c("start", "end", "center", "3p", "5p")` for a `GRanges` object.

### See Also

mutate, stretch

### Examples

    df <- data.frame(start = 1:10, width = 5)
    rng <- as_iranges(df)
    rng_by_start <- anchor_start(rng)
    rng_by_start
    anchor(rng_by_start)
    mutate(rng_by_start, width = 3L)
    grng <- as_granges(df,
                       seqnames = "chr1",
                       strand = c(rep("-", 5), rep("+", 5)))
    rng_by_5p <- anchor_5p(grng)
    rng_by_5p
    mutate(rng_by_5p, width = 3L)

[Package plyranges version 1.4.4 Index]