doAffineAlignmentCpp: Perform affine global and overlap alignment on a similarity...
In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

doAffineAlignmentCpp

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

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.