DNAmotifAlignment.Rd
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 |
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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)