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()){
        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)
        jaspar.scores <- MotIV::readDBScores(file.path(find.package("MotIV"),
                                       "extdata", "jaspar2010_PCC_SWU.scores"))
        d <- MotIV::motifDistances(pfms)
        hc <- MotIV::motifHclust(d, method="average")
        phylog <- hclust2phylog(hc)
        reorderUPGMAtree(phylog, pfms)
      }

[Package motifStack version 1.28.0 Index]