exportAsRangedData: Export MotIV Results

In alyst/MotIV: Motif Identification and Validation

Description

Export your

Usage

exportAsRangedData(x, y, correction=TRUE)

Arguments

x	An object of class motiv.
y	The rGADEM type object associated with the motiv object.
correction	If TRUE, corrects the position according to the alignment.

Details

Use this function to export the results into a RangedData object.

Value

An object of type RangedData.

Author(s)

Eloi Mercier <[e-mail]>

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)

#####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))

#####RangedData#####
foxa1.rd <- exportAsRangedData(foxa1.filter.combine["FOXA1"], gadem)
ap1.rd <- exportAsRangedData(foxa1.filter.combine["AP1"], gadem)

alyst/MotIV documentation built on May 12, 2019, 2:33 a.m.