reorderUPGMAtree {motifStack} | R Documentation

## re-order UPGMA tree

### Description

re-order the UPGMA tree by adjacent motif distance

### Usage

    reorderUPGMAtree(phylog, motifs, rcpostfix = "(RC)")

### Arguments

`phylog` | an object of phylog
`motifs` | a list of objects of pfm
`rcpostfix` | the postfix for reverse complements

### Value

an object of phylog

### Author(s)

Jianhong Ou

### 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)
        pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                     new("pfm",mat=.ele, name=.name)})
        reorderUPGMAtree(phylog, pfms)
      }

[Package motifStack version 1.34.0 Index]