setFilter {MotIV} | R Documentation |
This function is use to set a motif filter.
setFilter(name="", tfname="",evalueMax=1, top=10, lengthMax=100,valid=NULL)
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. |
A filter
object.
Eloi Mercier <emercier@chibi.ubc.ca>
filter
, split
, combine
#####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)