mergeMotifs {circRNAprofiler} | R Documentation

## Group motifs shared by multiple RBPs

### Description

A same RBP can recognize multiple motifs, the function mergeMotifs() groups all the motifs found for each RBP and report the total counts.

### Usage

    mergeMotifs(motifs)

### Arguments

`motifs` | A data frame generated with `getMotifs`.

### Value

A data frame.

### Examples

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

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

    # Example with the first back-spliced junctions.
    # Multiple back-spliced junctions can also be analyzed at the same time.

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

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

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

    # Get motifs
    motifs <-
    getMotifs(
        targets,
        width = 6,
        species = "Hsapiens",
        rbp = TRUE,
        reverse = FALSE)

    # Group motifs
    mergedMotifs <- mergeMotifs(motifs)

[Package circRNAprofiler version 1.6.0 Index]