getRankedUniqueMotifs {motifStack} | R Documentation

## 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)
        }

[Package motifStack version 1.36.1 Index]