geneAnnotation {RLSeq} | R Documentation

## Annotate R-Loops with Genes

### Description

Annotates RLRanges with entrez ids for overlapping genes. See details.

### Usage

    geneAnnotation(object, txdb = NULL)

### Arguments

`object` | An RLRanges object.
`txdb` | The TxDb or EnsDb object containing gene annotations. If not supplied, annotations will be automatically downloaded from AnnotationHub. See also GenomicFeatures::TxDb.

### Details

The `geneAnnotation` function provides a simple procedure for annotating RLRanges with gene IDs by overlap.

#### Annotations

First. gene annotations are automatically downloaded using AnnotationHub::query with the following pattern:

    AnnotationHub::query(
        x = ah,
        pattern = c("TxDb", "UCSC", "knownGene", genome)
    )

Where `genome` is the UCSC genome id for the RLRanges object. If these annotations are unavailable, they should be provded using the `txdb` parameter. See also GenomicFeatures::TxDb.

#### Overlaps

The annotations are subsequently overlapped with the ranges in the supplied RLRanges object using valr::bed_intersect and saved in the RLResults object as a `tbl` with a mapping of peak names to `gene_id` (entrez gene IDs).

### Value

An RLRanges object with gene overlaps included. The results are available via `rlresult(object, "geneAnnoRes")`. The result object is a `tbl` with a mapping of `peak_name` (peak names from `names(object)`) to `gene_id` (entrez gene IDs).

### Examples

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

    # Perform gene annotation
    rlr <- geneAnnotation(rlr)

    # Supply custom TxDb if needed
    if (GenomeInfoDb::genome(rlr)[1] == "hg19") {
        library(TxDb.Hsapiens.UCSC.hg19.knownGene)
        rlr <- geneAnnotation(rlr, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)
    }

[Package RLSeq version 1.0.0 Index]