exportAsTransfacFile {MotIV} | R Documentation

## Write Transfac Files

### Description

Export an object of class motiv as a Transfac file type.

### Usage

    	## S4 method for signature 'motiv'
    exportAsTransfacFile(x, file)
    	## S4 method for signature 'list'
    exportAsTransfacFile(x, file)

### Arguments

`x` | An object of class `motiv` to be export.
`file` | A character string naming a file.

### Details

This function is made to provide standard output file used by STAMP. It take an object of class `motiv` and write two files named `*_matched.txt` and `*_match_pairs.txt` containing alignments and identified PWMs.

For more information about the Transfac file format, please refere to http://www.benoslab.pitt.edu/stamp/help.html.

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

    #####Filters#####
    f.foxa1<-setFilter(name="", tfname="FOXA1", top=3, evalueMax=10^-5)
    f.ap1 <- setFilter (tfname="AP1", top=3)
    f.foxa1.ap1 <- f.foxa1 | f.ap1
    foxa1.filter <- filter(foxa1.analysis.jaspar, f.foxa1.ap1, exact=FALSE, verbose=TRUE)
    foxa1.split <- split(foxa1.analysis.jaspar, c(f.foxa1, f.ap1) , drop=FALSE, exact=FALSE, verbose=TRUE)
    foxa1.filter.combine <- combineMotifs(foxa1.filter, c(f.foxa1, f.ap1), exact=FALSE, name=c("FOXA1", "AP1"), verbose=TRUE)

    #####Export#####
    #exportAsTransfacFile(foxa1.filter.combine, file="foxa1_analysis")

[Package MotIV version 1.40.0 Index]