compareProfiles {motifStack} | R Documentation

## comapre w pcm

### Description

compare two pcm objects

### Usage

    compareProfiles(
      pcm1,
      pcm2,
      method = c("Smith-Waterman", "Needleman-Wunsch"),
      pseudo = 1,
      revcomp = TRUE
    )

### Arguments

`pcm1, pcm2` | object of pcm
`method` | Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
`pseudo` | pseudocount
`revcomp` | Check reverseComplement or not.

### Value

a list with names: motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.

[Package motifStack version 1.36.1 Index]