rlRegionTest {RLSeq} | R Documentation

## R-Loop region test

### Description

Tests the overlap of user-supplied ranges with R-loop regions (RL regions).

### Usage

    rlRegionTest(object)

### Arguments

`object` | An RLRanges object with genome "hg38".

### Details

R-loop regions (RL regions) are consensus sites of R-loop formation. For more information, see RLHub::rlregions. The `rlRegionTest` is a simple function which finds the overlap of user-supplied samples with RL regions and calculates Fisher's exact test via valr::bed_fisher.

### Value

An RLRanges object with test results accessible via `rlresult(object, "rlRegionRes")`.

#### Structure

The structure of the results is a named `list` containing the following:

- `Overlap`

  - A `tbl` showing the overlap between RL regions and user-supplied ranges.

  - Column description:

    - `chrom` - The chromosome name

    - `start__peaks` - The starting position of the user-supplied peak in the overlap.

    - `end__peaks` - Same as above for end position.

    - `name__peaks` - The name of the user-supplied peak in the overlap (from `names(object)`).

    - `start/end/name__rlregion` - Same as above for RL regions.

    - `strand__rlregion` - The genomic strand of the RL region in the overlap.

    - `.overlap` - The size of the overlap.

- `Test_results`

  - A `tbl` showing the results of the Fisher's exact test. See valr::bed_fisher.

### Examples

    # Example RLRanges data
    rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))

    # RL Region Test
    rlRegionTest(rlr)

[Package RLSeq version 1.0.0 Index]