getSeqSimMatCpp: Calculates similarity matrix for two sequences

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Calculates similarity matrix for two sequences

Usage

getSeqSimMatCpp(seq1, seq2, match, misMatch)

Arguments

seq1	(char) A single string.
seq2	(char) A single string.
match	(double) Score for character match.
misMatch	(double) score for character mismatch.

Value

s (matrix) Numeric similarity matrix. Rows and columns expresses seq1 and seq2, respectively.

Author(s)

Shubham Gupta, [e-mail] ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-05

Examples

# Get sequence similarity of two DNA strings
Match=10; MisMatch=-2
seq1 = "GCAT"; seq2 = "CAGTG"
getSeqSimMatCpp(seq1, seq2, Match, MisMatch)
matrix(c(-2, 10, -2, -2, -2, -2, 10, -2, 10, -2, -2, -2, -2, -2, -2, 10, 10, -2, -2, -2),
 4, 5, byrow = FALSE)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.