refine_ERs {ODER} | R Documentation

## Refines the ERs start and end points

### Description

Uses the junctions added by `annotatERs` to modify the starts and ends of the expressed regions. When a junction intersects an expressed region depending on whether it is the start or end or both, the regions corresponding starts and ends will be modified.

### Usage

    refine_ERs(annot_ers)

### Arguments

`annot_ers` | ERs that have been annotated (result of annotatER)

### Details

As junctions mark intron boundaries, the expressed region will be changed to either being one less or one more than the junction end.

### Value

Genomic ranges with refined base pair starts and ends

### Examples

    # create example set of ers to save runtime
    ex_annot_ers <- GenomicRanges::GRanges(
        seqnames = S4Vectors::Rle(c("chr21"), c(3)),
        ranges = IRanges::IRanges(
            start = c(5093576, 5097663, 5162182),
            end = c(5093833, 5097762, 5162257)
        ),
        grl = GenomicRanges::GRangesList(
            GenomicRanges::GRangesList(
                GenomicRanges::GRanges(
                    seqnames = S4Vectors::Rle(c("chr21"), c(1)),
                    ranges = IRanges::IRanges(
                        start = c(5093712),
                        end = c(5093744)
                    )
                ),
                GenomicRanges::GRanges(
                    seqnames = S4Vectors::Rle(c("chr21"), c(1)),
                    ranges = IRanges::IRanges(
                        start = c(5097642),
                        end = c(5097669)
                    )
                ),
                GenomicRanges::GRanges(
                    seqnames = S4Vectors::Rle(c("chr21"), c(1)),
                    ranges = IRanges::IRanges(
                        start = c(5162249),
                        end = c(5162287)
                    )
                )
            )
        ),
        annotation = c("intron", "intron", "intron")
    )

    refined_ers <- refine_ERs(ex_annot_ers)

    refined_ers

[Package ODER version 1.0.0 Index]