exportAsTransfacFile {MotIV} | R Documentation |
Export an object of class motiv as a Transfac file type.
## S4 method for signature 'motiv' exportAsTransfacFile(x, file) ## S4 method for signature 'list' exportAsTransfacFile(x, file)
x |
An object of class |
file |
A character string naming a file. |
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.
Eloi Mercier <emercier@chibi.ubc.ca>
#####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")