doAlignmentCpp: Perform non-affine global and overlap alignment on a...

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

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, [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)
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)

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