doAffineAlignmentCpp {DIAlignR} | R Documentation

## Perform affine global and overlap alignment on a similarity matrix

### Description

Perform affine global and overlap alignment on a similarity matrix

### Usage

    doAffineAlignmentCpp(sim, go, ge, OverlapAlignment)

### Arguments

`sim` | (NumericMatrix) A numeric matrix with similarity values of two sequences or signals.
`go` | (numeric) Penalty for introducing first gap in alignment.
`ge` | (numeric) Penalty for introducing subsequent gaps in alignment.
`OverlapAlignment` | (logical) An input for alignment with free end-gaps. False: Global alignment, True: overlap alignment.

### Value

affineAlignObj (S4class) An object from C++ class of AffineAlignObj.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-08

### Examples

    # Get sequence similarity of two DNA strings
    Match=10; MisMatch=-2
    seq1 = "GCAT"; seq2 = "CAGTG"
    s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch)
    objAffine_Global <- doAffineAlignmentCpp(s, 22, 7, FALSE)
    slot(objAffine_Global, "score") # -2  -4  -6  4 -18
    objAffine_Olap <- doAffineAlignmentCpp(s, 22, 7, TRUE)
    slot(objAffine_Olap, "score") # 0 10 20 18 18 18

    Match=10; MisMatch=-2
    seq1 = "CAT"; seq2 = "CAGTG"
    s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch)
    objAffine_Global <- doAffineAlignmentCpp(s, 22, 7, FALSE)
    slot(objAffine_Global, "score") # 10  20  -2  -9 -11
    objAffine_Olap <- doAffineAlignmentCpp(s, 22, 7, TRUE)
    slot(objAffine_Olap, "score") # 10 20 18 18 18

    Match=10; MisMatch=-2
    seq1 = "CA"; seq2 = "AG"
    s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch)
    objAffine_Global <- doAffineAlignmentCpp(s, 22, 7, FALSE)
    slot(objAffine_Global, "simScore_forw") # -4

[Package DIAlignR version 0.99.12 Index]