reorderUPGMAtree {motifStack} | R Documentation |
re-order the UPGMA tree by adjacent motif distance
reorderUPGMAtree(phylog, motifs, rcpostfix = "(RC)")
phylog |
an object of phylog |
motifs |
a list of objects of pfm |
rcpostfix |
the postfix for reverse complements |
an object of phylog
Jianhong Ou
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) }