viewAlignments {MotIV} | R Documentation

## Print Motifs Alignments

### Description

This function return a list of the alignments of a motiv object for each motif.

### Usage

      viewAlignments(x)

### Arguments

`x` | An object of class motiv (usualy provied by motifMatch).

### Details

This function shows the alignements for each motif.

### Author(s)

Eloi Mercier <emercier@chibi.ubc.ca>

### See Also

`as.data.frame`

### 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)
    summary(foxa1.analysis.jaspar )
    viewAlignments(foxa1.analysis.jaspar )

[Package MotIV version 1.40.0 Index]