Write Transfac Files

Share:

Description

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

Usage

1
2
3
4
	## 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
#####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")