annotateRepeats {circRNAprofiler} | R Documentation

## Annotate repetitive elements

### Description

The function annotateRepeats() annotates repetitive elements located in the region flanking the back-spliced junctions of each circRNA. Repetitive elements are provided by AnnotationHub storage which collected repeats from RepeatMasker database. See `AnnotationHub` and http://www.repeatmasker.org for more details. An empty list is returned if none overlapping repeats are found.

### Usage

    annotateRepeats(targets, annotationHubID = "AH5122", complementary = TRUE)

### Arguments

`targets` | A list containing the target regions to analyze. It can be generated with `getSeqsFromGRs`.
`annotationHubID` | A string specifying the AnnotationHub id to use. Type data(ahRepeatMasker) to see all possible options. E.g. if AH5122 is specified, repetitive elements from Homo sapiens, genome hg19 will be downloaded and annotated. Default value is "AH5122".
`complementary` | A logical specifying whether to filter and report only back-spliced junctions of circRNAs which flanking introns contain complementary repeats, that is, repeats belonging to a same family but located on opposite strands.

### Value

A list.

### Examples

    # Load data frame containing detected back-spliced junctions
    data("mergedBSJunctions")

    # Load short version of the gencode v19 annotation file
    data("gtf")

    # Annotate the first back-spliced junctions
    annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)

    # Get genome
    if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)){

    genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

    # Retrieve targets
    targets <- getSeqsFromGRs(
        annotatedBSJs,
        genome,
        lIntron = 200,
        lExon = 10,
        type = "ie"
        )

    # Annotate repeats

     repeats <- annotateRepeats(targets, annotationHubID  = "AH5122",
     complementary = TRUE)

    }

[Package circRNAprofiler version 1.6.0 Index]