motifSignature: get signatures from motifs

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

get signatures from motifs

Description

extract signatures from multiple motifs by distance calculated from STAMP

Usage

motifSignature(
  pfms,
  phylog,
  cutoffPval,
  groupDistance,
  rcpostfix = "(RC)",
  min.freq = 2,
  trim = 0.2,
  families = list(),
  sort = TRUE
)

Arguments

pfms	a list of objects of class pfm
phylog	an object of class phylog
cutoffPval	pvalue for motifs to merge.
groupDistance	maxmal distance of motifs in the same group
rcpostfix	postfix for reverse-complement motif names, default: (RC)
min.freq	signatures with frequency below min.freq will not be plotted
trim	minimal information content for each position of signature
families	for each family, the motif number in one signature should only count as 1
sort	sort the signatures by frequency or not.

Value

an Object of class motifSig

Examples

  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
  }

jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.