align DNA motifs

align DNA motifs for plotting motifs stack

DNAmotifAlignment(
  pfms,
  threshold = 0.4,
  minimalConsensus = 0,
  rcpostfix = "(RC)",
  revcomp = rep(TRUE, length(pfms))
)

Arguments

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

Value

a list of aligned motifs

Examples

pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
motifs<-DNAmotifAlignment(motifs)