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()){
            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)
        }

[Package motifStack version 1.31.2 Index]