getMiRsites: Screen target sequences for miR binding sites

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

Description

The function getMirSites() searches miRNA binding sites within the circRNA sequences. The user can restrict the analisis only to a subset of miRs. In this case, miR ids must go in miR.txt file. If the latter is absent or empty, all miRs of the specified miRspeciesCode are considered in the analysis.

Usage

getMiRsites(
  targets,
  miRspeciesCode = "hsa",
  miRBaseLatestRelease = TRUE,
  totalMatches = 7,
  maxNonCanonicalMatches = 1,
  pathToMiRs = NULL
)

Arguments

targets	A list containing the target sequences to analyze. This data frame can be generated with getCircSeqs.
miRspeciesCode	A string specifying the species code (3 letters) as reported in miRBase db. E.g. to analyze the mouse microRNAs specify "mmu", to analyze the human microRNAs specify "hsa". Type data(miRspeciesCode) to see the available codes and the corresponding species reported in miRBase 22 release. Default value is "hsa".
miRBaseLatestRelease	A logical specifying whether to download the latest release of the mature sequences of the microRNAs from miRBase (http://www.mirbase.org/ftp.shtml). If TRUE is specified then the latest release is automatically downloaded. If FALSE is specified then a file named mature.fa containing fasta format sequences of all mature miRNA sequences previously downloaded by the user from mirBase must be present in the working directory. Default value is TRUE.
totalMatches	An integer specifying the total number of matches that have to be found between the seed region of the miR and the seed site of the target sequence. If the total number of matches found is less than the cut-off, the seed site is discarded. The maximun number of possible matches is 7. Default value is 7.
maxNonCanonicalMatches	An integer specifying the max number of non-canonical matches (G:U) allowed between the seed region of the miR and the seed site of the target sequence. If the max non-canonical matches found is greater than the cut-off, the seed site is discarded. Default value is 1.
pathToMiRs	A string containing the path to the miRs.txt file. The file miRs.txt contains the microRNA ids from miRBase specified by the user. It must have one column with header id. The first row must contain the miR name starting with the ">", e.g >hsa-miR-1-3p. The sequences of the miRs will be automatically retrieved from the mirBase latest release or from the given mature.fa file, that should be present in the working directory. By default pathToMiRs is set to NULL and the file it is searched in the working directory. If miRs.txt is located in a different directory then the path needs to be specified. If this file is absent or empty, all miRs of the specified species are considered in the miRNA analysis.

Value

A list.

Examples

# Load a 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 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 )
}

circRNAprofiler documentation built on March 6, 2021, 2 a.m.