alignS {obAnalytics} | R Documentation |
Align 2 sequences.
Description
Verbatim implementation of Needleman-Wunsch matching algorithm.
Usage
alignS(s.matrix, gap = -1)
Arguments
s.matrix |
Similarity matrix. See sMatrix(...). |
gap |
Penality assigned to a gap (missing or extra value). |
Value
2 column matrix. First column = similarity matrix rows (first sequence), Second column = similarity matrix columns (second sequence). Each row maps aligned indexs from each sequence:
> a <- c(2,4,5) > b <- 1:5 > alignS(sMatrix(a,b)) a b [1,] 1 2 [2,] 2 4 [3,] 3 5
Author(s)
phil
References
https://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm
Examples
## Not run:
a <- c(2,4,5)
b <- 1:5
alignS(sMatrix(a, b))
## End(Not run)
[Package obAnalytics version 0.1.1 Index]