indices2kaks: indices2kaks

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

indices2kaks

Description

This function calculates Ka/Ks (pN/pS) for all combinations given in an indices list of a DNAStringSet. If the sequences in the DNAStringSet are not a multiple-sequence alignment, pairwise codon alignments can be calculated on the fly. Models used and implemented according to Li (1993) (using seqinr) or Nei and Gojobori (1986) (own implementation) or models from KaKs_Calculator2 ported to MSA2dist with Rcpp.

Usage

indices2kaks(
  cds,
  indices,
  model = "Li",
  threads = 1,
  isMSA = TRUE,
  sgc = "1",
  verbose = FALSE,
  ...
)

Arguments

cds	DNAStringSet coding sequence alignment [mandatory]
indices	list list of indices to calculate Ks/Ks [mandatory]
model	specify codon model either "Li" or "NG86" or one of KaKs_Calculator2 model "NG", "LWL", "LPB", "MLWL", "MLPB", "GY", "YN", "MYN", "MS", "MA", "GNG", "GLWL", "GLPB", "GMLWL", "GMLPB", "GYN", "GMYN" [default: Li]
threads	number of parallel threads [default: 1]
isMSA	cds DNAStringSet represents MSA [default: TRUE]
sgc	standard genetic code (for KaKs Calculator models) [default: 1]
verbose	verbosity (for KaKs Calculator models) [default: FALSE]
...	other codon alignment parameters

Value

A data.frame of KaKs values

Author(s)

Kristian K Ullrich

References

"MS/MA/GNG/GLWL/GLPB/GMLWL/GMLPB/GYN:" Wang et al. (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.Genomics, proteomics & bioinformatics. 8(1), 77-80.

"Li/LWL:" Li et al. (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol., 2(2), 150-174.

"Li/LPB:" Li (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of molecular evolution, 36(1), pp.96-99.

"NG86/NG:" Nei and Gojobori. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3(5), 418-426.

"LPB:" Pamilo and Bianchi. (1993) Evolution of the Zfx and Zfy genes: Rates and interdependence between genes. Mol. Biol. Evol., 10, 271-281.

"MLWL/MLPB:" Tzeng et al. (2004). Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 21(12), 2290-2298.

"GY:" Goldman and Yang (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol., 11(5) 725-736.

"YN:" Yang et al. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155(1), 431-449.

"MYN:" Zhang et al. (2006). Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC evolutionary biology, 6(1), 1-10.

"data(hiv):" Ganeshan et al. (1997) Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virology. 71(1), 663-677.

Wang et al. (2009). gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biology Direct, 4(1), 1-18.

See Also

kaks

Examples

## load example sequence data
data("hiv", package="MSA2dist")
## create indices
idx <- list(c(2, 3), c(5,7,9))
#indices2kaks(hiv, idx, model="Li")
hiv |> indices2kaks(idx, model="Li")
#indices2kaks(hiv, idx, model="NG86")
hiv |> indices2kaks(idx, model="NG86")
#indices2kaks(hiv, idx, model="NG86", threads=2)
hiv |> indices2kaks(idx, model="NG86", threads=2)

## define three unaligned cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATGCATTGC")
cds3 <- Biostrings::DNAString("ATGCAATGC")
cds_sequences <- Biostrings::DNAStringSet(list(cds1, cds2, cds3))
names(cds_sequences) <- c("cds1", "cds2", "cds3")
## create indices
idx <- list(c(1, 2), c(1,3))
## set isMSA to FALSE to automatically create pairwise codon alignments
#indices2kaks(cds_sequences, idx, model="Li", isMSA=FALSE)
cds_sequences |> indices2kaks(idx, model="Li", isMSA=FALSE)

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.