setFilter {MotIV} | R Documentation

## Set Motif Filter

### Description

This function is use to set a motif filter.

### Usage

      setFilter(name="", tfname="",evalueMax=1, top=10, lengthMax=100,valid=NULL)

### Arguments

`name` | A name or a list of names.
`tfname` | A transcription factor name or a list of TF names.
`evalueMax` | An evalue between 0 and 1.
`top` | Defines the depth of the filter.
`lengthMax` | The maximum motif length.
`valid` | The alignment that should be considered as valid.

### Value

A `filter` object.

### Author(s)

Eloi Mercier <emercier@chibi.ubc.ca>

### See Also

`filter` , `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)

[Package MotIV version 1.40.0 Index]