motifStack (version 1.16.2)

DNAmotifAlignment: align DNA motifs

Description

align DNA motifs for plotting motifs stack

Usage

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

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)