viewAlignments {MotIV} | R Documentation |
This function return a list of the alignments of a motiv object for each motif.
viewAlignments(x)
x |
An object of class motiv (usualy provied by motifMatch). |
This function shows the alignements for each motif.
Eloi Mercier <emercier@chibi.ubc.ca>
as.data.frame
#####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 ) viewAlignments(foxa1.analysis.jaspar )