saveAlignments {enhancerHomologSearch} | R Documentation

## output alignments

### Description

Save enhancer homologs to file in phylip format.

### Usage

    saveAlignments(al, output_folder = tempdir(), motifConsensus = NULL)

### Arguments

`al` | output of alignment.
`output_folder` | output folder.
`motifConsensus` | Transcription factor binding consensus.

### Value

The I/O status.

### Examples

    al <- readRDS(system.file("extdata", "al.rds",
                   package="enhancerHomologSearch"))
    tmpfolder <- tempdir()
    library(MotifDb)
    motifs <- query(MotifDb, "JASPAR_CORE")
    consensus <- sapply(motifs, consensusString)
    consensus <- DNAStringSet(gsub("\\?", "N", consensus))
    saveAlignments(al, output_folder=tmpfolder, motifConsensus=consensus)

[Package enhancerHomologSearch version 1.0.1 Index]