PFMSimilarity-methods {TFBSTools} | R Documentation

## PFMSimilarity method

### Description

Given a `PFMatrix` or a normal matrix, align it with another set of `PFMatrix` to assess the similarity.

### Usage

      PFMSimilarity(pfmSubject, pfmQuery, openPenalty=3, extPenalty=0.01)

### Arguments

`pfmSubject` | A `matrix`, `PFMatrix` or `PFMatrixList` object, which is compared with query matrix.
`pfmQuery` | A `matrix`, `PFMatrix` or IUPAC `character` object.
`openPenalty` | The gap open penalty used in the modified Needleman-Wunsch algorithm. By default, it is 3.
`extPenalty` | The gap extension penalty used in the modified Needleman-Wunsch algorithm. By default, it is 0.01.

### Value

For each `pfmSubject`, an absolute score and a relative percentage score is returned. The maximum absolute score is 2*the width of the smaller matrix in the comparison pair.

### Author(s)

Ge Tan

### References

Sandelin, A., H glund, A., Lenhard, B., & Wasserman, W. W. (2003). Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Functional & Integrative Genomics, 3(3), 125-134. doi:10.1007/s10142-003-0086-6

### Examples

      library(Biostrings)
      library(JASPAR2016)
      ## Example matrix from JASPAR database
      profileMatrix <- matrix(as.integer(
        c(13, 13,  3,  1, 54,  1,  1,  1,  0,  3,  2,  5,
          13, 39,  5, 53,  0,  1, 50,  1,  0, 37,  0, 17,
          17,  2, 37,  0,  0, 52,  3,  0, 53,  8, 37, 12,
          11,  0,  9,  0,  0,  0,  0, 52,  1,  6, 15, 20)),
        nrow=4, byrow=TRUE, dimnames=list(DNA_BASES))
      pfmQuery <- PFMatrix(profileMatrix=profileMatrix)
      pfmSubjects <- getMatrixSet(JASPAR2016,
                                  opts=list(ID=c("MA0500", "MA0499", "MA0521",
                                                 "MA0697", "MA0048", "MA0751",
                                                 "MA0832")))
      PFMSimilarity(pfmSubjects, pfmQuery)

[Package TFBSTools version 1.18.0 Index]