mergeMotifs: Group motifs shared by multiple RBPs

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

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)

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