Description Usage Arguments Value Examples

This function calculates three matrices for affine gap alignment using input similarity matrix and affine gap opening and gap closing penalties. An implementation of Needleman-Wunsch alignment and overlap alignment is also provided. All three matrices are clubbed together in an output S4 object.

1 | ```
getAffineAlignObj(s, go, ge, FreeEndGaps = TRUE)
``` |

`s` |
A numeric matrix |

`go` |
A numeric value |

`ge` |
A numeric value |

`FreeEndGaps` |
A logical scalar |

A S4 object

1 2 3 4 5 6 7 8 9 10 11 | ```
M = 10; MM = -2; go = 22; ge = 7
seq1 = "GCAT"
seq2 = "CAGTG"
s = matrix(NA, nrow = nchar(seq1), ncol= nchar(seq2))
for(i in 1:nrow(s)){
for(j in 1: ncol(s)){
if(substr(seq1, start = i, stop = i) == substr(seq2, start = j, stop = j)) s[i,j] <- M
else s[i,j] <- MM
}
}
alignObj <- getAffineAlignObj(s, go, ge, FreeEndGaps=FALSE)
``` |

shubham1637/DIAlignR documentation built on May 8, 2019, 8:12 a.m.

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