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 1.36.1 Index]