conservedMotifs: check the conserved motifs in the orthologs

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

check the conserved motifs in the orthologs

Description

Print the conserved motifs in the alignments

Usage

conservedMotifs(
  aln,
  aln_list,
  PWMs,
  queryGenome,
  background = "genome",
  ...,
  output_folder,
  format = c("txt", "html")
)

Arguments

aln	alignment of multiple DNAs. Output of alignment function.
aln_list	The list of output of searchTFBPS such as 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.
...	Other parameters can be passed to to matchMotifs.
output_folder	Output folder name.
format	The format of output files with motif match positions. Available formats are 'txt' and 'html'. Default is 'txt'.

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]], list(human=aln_hs, mouse=aln_mm),
                motifs[["dist60"]], Drerio)

jianhong/enhancerHomologSearch documentation built on Nov. 19, 2024, 11:13 p.m.