doAffineAlignmentCpp: Perform affine global and overlap alignment on a similarity...

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail] 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

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.