getRankedUniqueMotifs: get the unique motif in each category grouped by distance

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

get the unique motif in each category grouped by distance

Description

to get the unique motif in a given category, eg by species.

Usage

getRankedUniqueMotifs(phylog, attr)

Arguments

phylog	an object of class phylog
attr	attribute used for category of motifs

Value

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

Author(s)

Jianhong Ou

Examples

   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)
    }

jianhong/motifStack documentation built on May 8, 2024, 12:14 a.m.