conservedMotifs {enhancerHomologSearch}R Documentation

check the conserved motifs in the orthologs

Description

Print the conserved motifs in the alignments

Usage

conservedMotifs(aln, aln_hs, aln_mm, PWMs, queryGenome, background = "genome")

Arguments

aln

alignment of multiple DNAs. Output of alignment function.

aln_hs, aln_mm

output of linksearchTFBPS for human and mouse.

PWMs

The Position Weight Matrix list represented as a numeric matrix. Object of PWMatrixList or PFMatrixList.

queryGenome

An object of BSgenome for query enhancer.

background

background nucleotide frequencies. Default is "genome". Refer matchMotifs for details.

Value

A list of XStringviews.

Examples

library(BSgenome.Hsapiens.UCSC.hg38)
library(BSgenome.Mmusculus.UCSC.mm10)
library(BSgenome.Drerio.UCSC.danRer10)
LEN <- GRanges("chr4", IRanges(19050041, 19051709))
seqEN <- getSeq(BSgenome.Drerio.UCSC.danRer10, LEN)
aln_hs <- readRDS(system.file("extdata", "aln_hs.rds",
               package="enhancerHomologSearch"))
genome(aln_hs) <- Hsapiens
aln_mm <- readRDS(system.file("extdata", "aln_mm.rds",
               package="enhancerHomologSearch"))
genome(aln_mm) <- Mmusculus
al <- alignment(seqEN, list(human=aln_hs, mouse=aln_mm),
                method="ClustalW", order="input")
data(motifs)
conservedMotifs(al[[1]], aln_hs, aln_mm, motifs[["dist60"]], Drerio)

[Package enhancerHomologSearch version 1.0.0 Index]