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)

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