Description Usage Arguments Value Author(s) Examples
View source: R/reorderUPGMAtree.R
re-order the UPGMA tree by adjacent motif distance
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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)
}
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