| DNAmotifAlignment {motifStack} | R Documentation |
align DNA motifs for plotting motifs stack
DNAmotifAlignment(pfms, threshold=0.4, minimalConsensus=0,
rcpostfix="(RC)", revcomp=rep(TRUE, length(pfms)))
pfms |
a list of position frequency matrices, pfms must be a list of class pfm or psam |
threshold |
information content cutoff threshold for useful postions |
minimalConsensus |
minimal length of consensus for alignment |
rcpostfix |
the postfix for reverse complements |
revcomp |
a logical vector to indicates whether the reverse complemet should be involved into alignment |
a list of aligned motifs
pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
motifs<-DNAmotifAlignment(motifs)