getRankedUniqueMotifs {motifStack} | R Documentation |
to get the unique motif in a given category, eg by species.
getRankedUniqueMotifs(phylog, attr)
phylog |
an object of class phylog |
attr |
attribute used for category of motifs |
return a list:
uni.rank |
unique motif ranks |
uni.length |
length of unique motif grouped by distance |
uni.list |
unique motif names grouped by distance |
Jianhong Ou
if(interactive()){ library("MotifDb") matrix.fly <- query(MotifDb, "Dmelanogaster") matrix.human <- query(MotifDb, "Hsapiens") pfms <- c(as.list(matrix.fly), as.list(matrix.human)) pfms <- pfms[sample(1:length(pfms), 100)] 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$leaves) attr <- gsub("^(.*?)_.*$", "\1", leaves) getRankedUniqueMotifs(phylog, attr) }