doAlignmentCpp {DIAlignR} | R Documentation

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

### Description

Perform non-affine global and overlap alignment on a similarity matrix

### Usage

    doAlignmentCpp(sim, gap, OverlapAlignment)

### Arguments

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

### Value

AlignObj (S4class) An object from C++ class of AlignObj.

### 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)
    obj_Global <- doAlignmentCpp(s, 22, FALSE)
    slot(obj_Global, "score") # -2 -4 -6 4 -18
    obj_Olap <- doAlignmentCpp(s, 22, TRUE)
    slot(obj_Olap, "score") # 0 10 20 18 18 18

    Match=1; MisMatch=-1
    seq1 = "TTTC"; seq2 = "TGC"
    s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch)
    obj_Global <- doAlignmentCpp(s, 2, FALSE)
    slot(obj_Global, "optionalPaths")
    matrix(data = c(1,1,1,1,1,1,1,1,1,2,1,2,1,3,3,1,1,3,6,3), nrow = 5, ncol =4, byrow = TRUE)
    slot(obj_Global, "M_forw")
    matrix(data = c(0,-2,-4,-6,-2,-7,-22,-45,-4,-20,-72,-184,-6,-41,-178,-547,-8,-72,-366,-1274),
     nrow = 5, ncol =4, byrow = TRUE)

[Package DIAlignR version 0.99.12 Index]