SequenceSimilarity {SynExtend}

R Documentation

Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.

Description

Takes in a DNAStringSet or AAStringSet representing a pairwise alignment and a subsitution matrix such as those present in PFASUM, and return a numeric value representing sequence similarity as defined by the substitution matrix.

Usage

SequenceSimilarity(Seqs,
                   SubMat,
                   penalizeGapLetter = TRUE,
                   includeTerminalGaps = TRUE,
                   allowNegative = TRUE)

Arguments

Seqs	A DNAStringSet or AAStringSet of length 2.
SubMat	A named matrix representing a substitution matrix. If left “NULL” and “Seqs” is a AAStringSet, the 40th “PFASUM” matrix is used. If left “NULL” and “Seqs” is a DNAStringSet, a matrix with only the diagonal filled with “1”'s is used.
penalizeGapLetter	A logical indicating whether or not to penalize Gap-Letter matches. Defaults to “TRUE”.
includeTerminalGaps	A logical indicating whether or not to penalize terminal matches. Defaults to “TRUE”.
allowNegative	A logical indicating whether or not allow negative scores. Defaults to “TRUE”. If “FALSE” scores that are returned as less than zero are converted to zero.

Details

Takes in a DNAStringSet or AAStringSet representing a pairwise alignment and a subsitution matrix such as those present in PFASUM, and return a numeric value representing sequence similarity as defined by the substitution matrix.

Value

Returns a single numeric.

Author(s)

Erik Wright ESWRIGHT@pitt.edu Nicholas Cooley npc19@pitt.edu

See Also

AlignSeqs, AlignProfiles, AlignTranslation, DistanceMatrix

Examples

db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
dna <- SearchDB(db, remove="all")
alignedDNA <- AlignSeqs(dna[1:2])

DNAPlaceholder <- diag(15)
dimnames(DNAPlaceholder) <- list(DNA_ALPHABET[1:15],
                                 DNA_ALPHABET[1:15])

SequenceSimilarity(Seqs = alignedDNA,
                   SubMat = DNAPlaceholder,
                   includeTerminalGaps = TRUE,
                   penalizeGapLetter = TRUE,
                   allowNegative = TRUE)

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