viewMotifs-methods {MotIV} | R Documentation

## Print Identified Motifs

### Description

This function return a list of the identified motifs contained in a `motiv` object.

### Usage

    	## S4 method for signature 'motiv'
    viewMotifs(x,n=100)

### Arguments

`x` | An object of class motiv (usualy provied by motifMatch).
`n` | The number of motifs shown.

### Details

This function shows the number of identified motif.

### Value

A list of motifs names.

### Author(s)

Eloi Mercier <emercier@chibi.ubc.ca>

### Examples

    #####Database and Scores#####
    path <- system.file(package="MotIV")
    jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
    jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))

    #####Input#####
    data(FOXA1_rGADEM)
    motifs <- getPWM(gadem)
    motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)

    #####Analysis#####
    foxa1.analysis.jaspar <- motifMatch(inputPWM=motifs,align="SWU",cc="PCC",database=jaspar,DBscores=jaspar.scores,top=5)
    viewMotifs(foxa1.analysis.jaspar, 5)

[Package MotIV version 1.38.0 Index]