rcpp_KaKs

calculates KaKs as implememted in KaKs Calculator 2.0 MSA2dist with Rcpp.

rcpp_KaKs(cdsstr, sgc = "1", method = "YN", verbose = FALSE)

Arguments

cdsstr

StringVector [mandatory]

sgc

standard genetic code to use [default: 1]

method

KaKs Calculator 2.0 codon model [default: YN]

verbose

specify if verbose output [default: FALSE]

Value

list

References

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.

Author

Kristian K Ullrich

Examples

## load example sequence data
data("hiv", package="MSA2dist")
rcpp_KaKs(cdsstr=as.character(hiv[1:3]))
#> $rownames
#>  [1] "Comp1"                                               
#>  [2] "Comp2"                                               
#>  [3] "seq1"                                                
#>  [4] "seq2"                                                
#>  [5] "Method"                                              
#>  [6] "Ka"                                                  
#>  [7] "Ks"                                                  
#>  [8] "Ka/Ks"                                               
#>  [9] "P-Value(Fisher)"                                     
#> [10] "Length"                                              
#> [11] "S-Sites"                                             
#> [12] "N-Sites"                                             
#> [13] "Fold-Sites(0:2:4)"                                   
#> [14] "Substitutions"                                       
#> [15] "S-Substitutions"                                     
#> [16] "N-Substitutions"                                     
#> [17] "Fold-S-Substitutions(0:2:4)"                         
#> [18] "Fold-N-Substitutions(0:2:4)"                         
#> [19] "Divergence-Time"                                     
#> [20] "Substitution-Rate-Ratio(rTC:rAG:rTA:rCG:rTG:rCA/rCA)"
#> [21] "GC(1:2:3)"                                           
#> [22] "ML-Score"                                            
#> [23] "AICc"                                                
#> [24] "Akaike-Weight"                                       
#> [25] "Model"                                               
#> 
#> $results_vec
#> [1] "1\t2\tU68496\tU68497\tYN\t0.0259337\t0.0848079\t0.305794\t0.110988\t273\t37.4117\t235.588\tNA\t9\t3\t6\tNA\tNA\t0.0340018\t2.90975:2.90975:1:1:1:1\t0.300366(0.362637:0.368132:0.17033)\tNA\tNA\tNA\tNA"           
#> [2] "1\t3\tU68496\tU68498\tYN\t0.0833439\t0.0402529\t2.07051\t0.441303\t273\t36.6562\t236.344\tNA\t20\t1.42507\t18.5749\tNA\tNA\t0.077558\t2.92242:2.92242:1:1:1:1\t0.305861(0.373626:0.373626:0.17033)\tNA\tNA\tNA\tNA"
#> [3] "2\t3\tU68497\tU68498\tYN\t0.104384\t0.0325135\t3.21047\t0.19413\t273\t37.4724\t235.528\tNA\t24\t1.18051\t22.8195\tNA\tNA\t0.0945188\t3.99769:3.99769:1:1:1:1\t0.309524(0.373626:0.379121:0.175824)\tNA\tNA\tNA\tNA"
#> 
#> $results_names
#> [1] "U68496_U68497" "U68496_U68498" "U68497_U68498"
#>