filter: Filter Motifs

In MotIV: Motif Identification and Validation

Description

This function selects motifs according to a set of filters.

Usage

## S4 method for signature 'motiv,filters'
filter(x, f, exact=FALSE, verbose=TRUE)

Arguments

x	An object of class motiv.
f	A filter or a set of filter for motiv object.
verbose	If FALSE, no output will be print.
exact	If TRUE, search only for perfect name match.

Details

This function is used to select motifs that correspond to the filters.

Many filter could be pass in argument separated by coma. They will be considered independently.

Value

A motiv object.

Author(s)

Eloi Mercier <[e-mail]>

See Also

setFilter , split, combine

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)

MotIV documentation built on April 28, 2020, 6:51 p.m.