matalign {motifStack} | R Documentation

## Matrix Aligner

### Description

Matrix Aligner is modified from Matalign-v4a. Matalign-v4a is a program to compare two positional specific matrices. The author of Matalign-v4a is Ting Wang and Gary Stormo.

### Usage

    matalign(
      pcms,
      method = c("Smith-Waterman", "Needleman-Wunsch"),
      pseudo = 1,
      revcomp = TRUE,
      ...
    )

### Arguments

`pcms` | A list of pcm
`method` | Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
`pseudo` | pseudocount
`revcomp` | Check reverseComplement or not.
`...` | Not use.

### Value

A data frame with alignment information. The column names are motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.

### Examples

    if(interactive() || Sys.getenv("USER")=="jianhongou"){
      fp <- system.file("extdata", package="motifStack")
      fs <- dir(fp, "pcm$")
      pcms <- importMatrix(file.path(fp, fs), format="pcm")
      matalign(pcms)
     }

[Package motifStack version 1.36.1 Index]