DNAmotifAlignment {motifStack} | R Documentation

## 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 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)

[Package motifStack version 1.28.0 Index]