rlRegionTest: R-Loop region test

In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

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)

Bishop-Laboratory/RLSeq documentation built on Jan. 28, 2023, 11:38 p.m.