rearrangeMiRres {circRNAprofiler} | R Documentation

## Rearrange miR results

### Description

The function rearrangeMiRres() rearranges the results of the getMiRsites() function. Each element of the list contains the miR results relative to one circRNA. For each circRNA only miRNAs for which at least 1 miRNA binding site is found are reported.

### Usage

    rearrangeMiRres(miRsites)

### Arguments

`miRsites` | A list containing the miR sites found in the RNA target sequence. it can be generated with `getMiRsites`.

### Value

A list.

### Examples

    # Load data frame containing predicted 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
    genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

    # Retrieve target sequences.
     targets <- getCircSeqs(
         annotatedBSJs,
         gtf,
         genome)

    # Screen target sequence for miR binding sites.
    pathToMiRs <- system.file("extdata", "miRs.txt",package="circRNAprofiler")

    # miRsites <- getMiRsites(
    #    targets,
    #    miRspeciesCode = "hsa",
    #    miRBaseLatestRelease = TRUE,
    #    totalMatches = 6,
    #    maxNonCanonicalMatches = 1,
    #    pathToMiRs)

    # Rearrange miR results
    # rearragedMiRres <- rearrangeMiRres(miRsites)

[Package circRNAprofiler version 1.1.0 Index]