exportAsGRanges {MotIV} | R Documentation |
Export your
exportAsGRanges(x, y, correction=TRUE)
x |
An object of class |
y |
The rGADEM type object associated with the |
correction |
If |
Use this function to export the results into a GRanges
object.
An object of type GRanges
.
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) #####Plots##### #plot(foxa1.filter.combine, ncol=2,top=5, rev=FALSE, main="FOXA1", bysim=TRUE) #plot(foxa1.filter.combine ,gadem,ncol=2, type="distribution", correction=TRUE, group=FALSE, bysim=TRUE, strand=FALSE, sort=TRUE, main="FOXA1") #plot(foxa1.filter.combine ,gadem,type="distance", correction=TRUE, group=TRUE, bysim=TRUE, main="FOXA1", strand=FALSE, method=3, xlim=c(-100,100), darg=list(bw=8)) #####GRanges##### foxa1.gr <- exportAsGRanges(foxa1.filter.combine["FOXA1"], gadem) ap1.gr <- exportAsGRanges(foxa1.filter.combine["AP1"], gadem)