motifSignature {motifStack} | R Documentation

## get signatures from motifs

### Description

extract signatures from multiple motifs by distance calculated from STAMP

### Usage

    motifSignature(pfms, phylog, 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
`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()){
        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(lapply(pfms, pfm2pwm))
        hc <- MotIV::motifHclust(d, method="average")
        phylog <- hclust2phylog(hc)
        leaves <- names(phylog$leaves)
        pfms <- pfms[leaves]
        pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]],
                                                         name=.ele)},pfms)
        motifSig <- motifSignature(pfms, phylog, groupDistance=0.1)
      }

[Package motifStack version 1.28.0 Index]