ApproximateBackground: Return the approximate background alignment score for a...

In npcooley/SynExtend: Tools for Comparative Genomics

Return the approximate background alignment score for a series of paired sequences.

Description

This function is designed to work internally to SummarizePairs so it works on relatively simple atomic vectors and has little overhead checking.

Usage

ApproximateBackground(p1,
                      p2,
                      code1,
                      code2,
                      mod1,
                      mod2,
                      aa1,
                      aa2,
                      nt1,
                      nt2,
                      register1,
                      register2,
                      aamat,
                      ntmat)

Arguments

p1	Integer; references positions within nt1 or aa1.
p2	Integer; references positions within nt2 or aa2.
code1	Logical; specifies whether the position referenced by p1 is reported as a coding sequence.
code2	Logical; specifies whether the position referenced by p2 is reported as a coding sequence.
mod1	Logical; specifies whether the position referenced by p1 can be translated without complaint by translate.
mod2	Logical; specifies whether the position referenced by p2 can be translated without complaint by translate.
aa1	AAStringSet.
aa2	AAStringSet.
nt1	DNAStringSet.
nt2	DNAStringSet.
register1	Integer; a vector that maps which positions in aa1 are the translations of that particular index in nt1. NAs identify positions that are not translated.
register2	Integer; a vector that maps which positions in aa2 are the translations of that particular index in nt2. NAs identify positions that are not translated.
aamat	A substitution matrix for amino acids.
ntmat	A substitution matrix for nucleotides.

Details

ApproximateBackground generates approximate background alignment scores for sets of sequences.

Value

A vector of numerics.

Author(s)

Nicholas Cooley [e-mail]

See Also

NucleotideOverlap, SummarizePairs, FindSynteny

Examples

fas <- system.file("extdata", "50S_ribosomal_protein_L2.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
aa <- translate(dna)

s1 <- sample(x = length(dna),
             size = 30,
             replace = FALSE)
s2 <- s1[1:15]
s1 <- s1[16:30]

mat1 <- DECIPHER:::.getSubMatrix("PFASUM50")
mat2 <- DECIPHER:::.nucleotideSubstitutionMatrix(2L, -1L, 1L)

aa1 <- aa2 <- alphabetFrequency(aa)
aa1 <- aa2 <- aa1[, colnames(mat1)]
aa1 <- aa2 <- aa1 / rowSums(aa1)

nt1 <- nt2 <- alphabetFrequency(dna)
nt1 <- nt2 <- nt1[, colnames(mat2)]
nt1 <- nt2 <- nt1 / rowSums(nt1)

x <- ApproximateBackground(p1 = s1,
                           p2 = s2,
                           code1 = rep(TRUE, length(s1)),
                           code2 = rep(TRUE, length(s2)),
                           mod1 = rep(TRUE, length(s1)),
                           mod2 = rep(TRUE, length(s2)),
                           aa1 = aa1,
                           aa2 = aa2,
                           nt1 = nt1,
                           nt2 = nt2,
                           register1 = seq(length(dna)),
                           register2 = seq(length(dna)),
                           aamat = mat1,
                           ntmat = mat2)

npcooley/SynExtend documentation built on June 8, 2025, 5:24 a.m.