PFMSimilarity-methods {TFBSTools} | R Documentation |
Given a PFMatrix
or a normal matrix,
align it with another set of PFMatrix
to assess the similarity.
PFMSimilarity(pfmSubject, pfmQuery, openPenalty=3, extPenalty=0.01)
pfmSubject |
A |
pfmQuery |
A |
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. |
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.
Ge Tan
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
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)