setFilter: Set Motif Filter

In alyst/MotIV: Motif Identification and Validation

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 <[e-mail]>

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)

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