rearrangeMiRres: Rearrange miR results

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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)

Aufiero/circRNAprofiler documentation built on Nov. 3, 2024, 10:12 a.m.