SequenceSimilarity: Return a numeric value that represents the similarity between...

In npcooley/SynExtend: Tools for Working With Synteny Objects

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 [e-mail] Nicholas Cooley [e-mail]

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)

npcooley/SynExtend documentation built on Dec. 20, 2024, 4:03 p.m.