Description Usage Arguments Details Value Author(s) See Also Examples
This function splits a 'motiv' object according filters.
1 2 |
x |
An object of class motiv (usualy provied by motifMatch). |
f |
A filter or a set of filter for motiv object. |
drop |
If |
verbose |
If |
exact |
If |
... |
Further potential arguments passed to methods. |
This function is used to split motifs that correspond to the filters.
Many filter
could be pass in argument separated by coma. They will be considered independently (coma is considered as OR
).
A list of motiv
object.
Eloi Mercier <emercier@chibi.ubc.ca>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | #####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)
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