motifProfile: motifProfile for the GRanges objects

In Codezy99/cliProfiler: A package for the CLIP data visualization

Description

An function to plot the frequency or fraction of the interested motif around the center of input peaks.

Usage

motifProfile(
    object,
    motif = NA,
    genome = NA,
    fraction = TRUE,
    title = "Motif Profile",
    flanking = 10
)

Arguments

object	A GRanges object which should contains all the peaks that you want to check
motif	A character string which use the IUPAC nucleotide code, e.g. DRACH, TTAGGG.
genome	The name of the full genome sequences package in the Bioconductor, e.g. "BSgenome.Mmusculus.UCSC.mm10". You should install the package before running this function.
fraction	A logical vector (TRUE or FALSE) that the result should be presented in fraction or number.
title	The main title for the output meta gene profile plot.
flanking	The size of the flanking windows that you would like to check. Flanking=5 will give you the result of the 10+1nt windows around the center of peaks.

Value

A list object, the list 1 contains the information of the frequency of specified motif around the center of peaks. The list 2 includes the plot of motifProfile.

Author(s)

You Zhou, Kathi Zarnack

Examples

## Load the test data and get the path to the test gff3 file
testpath <- system.file("extdata", package = "cliProfiler")
test <- readRDS(file.path(testpath, "test.rds"))
test_gff3 <- file.path(testpath, "annotation_test.gff3")

## Please make sure that the correct BSgenome package have installed before
## running motifProfile. For example,library("BSgenome.Mmusculus.UCSC.mm10")
## would be required for the mouse data.

output <- motifProfile(test,
    motif = "DRACH",
    genome = "BSgenome.Mmusculus.UCSC.mm10",
    flanking = 20
)

Codezy99/cliProfiler documentation built on Dec. 17, 2021, 2:59 p.m.