doAffineAlignment_S4: Perform affine global and overlap alignment on a similarity...

Description Usage Arguments Value Author(s) Examples

Description

Perform affine global and overlap alignment on a similarity matrix

Usage

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doAffineAlignment_S4(s, signalA_len, signalB_len, go, ge, OverlapAlignment)

Arguments

s

(NumericMatrix) A numeric matrix with similarity values of two sequences or signals

signalA_len

(int) Length of signalA or sequenceA. Expresses along the rows of s

signalB_len

(int) Length of signalB or sequenceB. Expresses along the columns of s

go

(float) Penalty for introducing first gap in alignment

ge

(float) Penalty for introducing subsequent gaps in alignment

OverlapAlignment

(bool) 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, [email protected] ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-08

Examples

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# Get sequence similarity of two DNA strings
Match=10; MisMatch=-2
seq1 = "GCAT"; seq2 = "CAGTG"
s <- getSeqSimMat(seq1, seq2, Match, MisMatch)
objAffine_Global <- doAffineAlignment_S4(s, 4, 5, 22, 7, FALSE)
objAffine_Global@score # -2  -4  -6  4 -18
objAffine_Olap <- doAffineAlignment_S4(s, 4, 5, 22, 7, TRUE)
objAffine_Olap@score # 0 10 20 18 18 18

seq1 = "CAT"; seq2 = "CAGTG"
s <- getSeqSimMat(seq1, seq2, Match, MisMatch)
objAffine_Global <- doAffineAlignment_S4(s, 3, 5, 22, 7, FALSE)
objAffine_Global@score # 10  20  -2  -9 -11
objAffine_Olap <- doAffineAlignment_S4(s, 3, 5, 22, 7, TRUE)
objAffine_Olap@score # 10 20 18 18 18

shubham1637/DIAlignR documentation built on May 8, 2019, 8:12 a.m.