getSeqSimMatCpp {DIAlignR} | R Documentation

## Calculates similarity matrix for two sequences

### 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, shubh.gupta@mail.utoronto.ca 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)

[Package DIAlignR version 2.2.0 Index]