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 1.0.1 Index]