Description Usage Arguments Value Author(s) Examples
View source: R/getRankedUniqueMotifs.R
to get the unique motif in a given category, eg by species.
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 | if(interactive() || Sys.getenv("USER")=="jianhongou"){
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(seq_along(pfms), 100)]
hc <- clusterMotifs(pfms)
library(ade4)
phylog <- ade4::hclust2phylog(hc)
leaves <- names(phylog$leaves)
attr <- gsub("^(.*?)_.*$", "\1", leaves)
getRankedUniqueMotifs(phylog, attr)
}
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