output alignments

Save enhancer homologs to file in phylip format.

saveAlignments(
  al,
  output_folder = tempdir(),
  motifConsensus = NULL,
  format = c("txt", "html")
)

Arguments

al

output of alignment.

output_folder

output folder.

motifConsensus

Transcription factor binding consensus.

format

The format of output files. Available formats are 'txt' and 'html'. Default is 'txt'.

Value

The I/O status.

Examples

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