Combine Motifs

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Description

This function combines motifs according to a set of filters.

Usage

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## S4 method for signature 'motiv,filters'
combineMotifs(x, y, name=NULL,exact=TRUE,verbose=TRUE)

Arguments

x

An object of class motiv.

y

A filter or a set of filter.

name

Name(s) to be given for similar motifs.

verbose

If FALSE, no output will be print.

exact

If TRUE, search only for perfect name match.

Details

This function is used to consider some motifs as a unique motif or similar motifs.

Many filters could be pass in argument separated by coma. They will be considered independently (coma is considered as OR).

If a name or a vector of name is provided, it will be used to assign new name for similar motif to the corresponding filter. Else, a generic name is used.

Value

A motiv object.

Author(s)

Eloi Mercier <emercier@chibi.ubc.ca>

See Also

setFilter , filter, split

Examples

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#####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.filter.combine <- combineMotifs(foxa1.filter, c(f.foxa1, f.ap1), exact=FALSE, name=c("FOXA1", "AP1"), verbose=TRUE)