saveAlignments: output alignments

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

output alignments

Description

Save enhancer homologs to file in phylip format.

Usage

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)
motifs <- query(MotifDb, "JASPAR_CORE")
consensus <- sapply(motifs, consensusString)
consensus <- DNAStringSet(gsub("\\?", "N", consensus))
saveAlignments(al, output_folder=tmpfolder, motifConsensus=consensus)

jianhong/enhancerHomologSearch documentation built on Nov. 4, 2024, 8:29 p.m.