motifSignature {motifStack} | R Documentation

## 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)
      }

[Package motifStack version 1.34.0 Index]