rbh2kaks

This function calculates Ka/Ks (dN/dS; accoring to Li (1993) or Yang and Nielson (2000) for each (conditional-)reciprocal best hit (CRBHit) pair. The names of the rbh columns must match the names of the corresponding cds1 and cds2 DNAStringSet vectors.

Usage

rbh2kaks(
  rbhpairs,
  cds1,
  cds2,
  model = "Li",
  plotHistPlot = FALSE,
  plotDotPlot = FALSE,
  dag = NULL,
  gene.position.cds1 = NULL,
  gene.position.cds2 = NULL,
  tandem.dups.cds1 = NULL,
  tandem.dups.cds2 = NULL,
  colorBy = "none",
  threads = 1,
  ...
)

Arguments

rbhpairs: (conditional-)reciprocal best hit (CRBHit) pair result (see cds2rbh) [mandatory]
cds1: cds1 sequences as DNAStringSet or url for first crbh pairs column [mandatory]
cds2: cds2 sequences as DNAStringSet or url for second crbh pairs column [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]
plotHistPlot: specify if histogram should be plotted [default: TRUE]
plotDotPlot: specify if dotplot should be plotted (mandatory to define gene.position.cds1 and gene.position.cds1) [default: FALSE]
dag: specify DAGchainer results as obtained via `rbh2dagchainer()` [default: NULL]
gene.position.cds1: specify gene position for cds1 sequences (see cds2genepos) [default: NULL]
gene.position.cds2: specify gene position for cds2 sequences (see cds2genepos) [default: NULL]
tandem.dups.cds1: specify tandem duplicates for cds1 sequences (see tandemdups) [default: NULL]
tandem.dups.cds2: specify tandem duplicates for cds2 sequences (see tandemdups) [default: NULL]
colorBy: specify if Ka/Ks gene pairs should be colored by "rbh_class", dagchainer", "tandemdups" or "none" [default: none]
threads: number of parallel threads [default: 1]
...: other codon alignment parameters (see cds2codonaln) and other plot_kaks parameters (see plot_kaks)

Value

Ka/Ks values

References

Li WH. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol., 36, 96-99.

Wang D, Zhang Y et al. (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 8(1), 77-80.

Yang Z and Nielson R. (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol., 17(1), 32-43.

Author

Kristian K Ullrich

Examples

## load example sequence data
data("ath", package="CRBHits")
data("aly", package="CRBHits")
## load example CRBHit pairs
data("ath_aly_crbh", package="CRBHits")
## only analyse subset of CRBHit pairs
ath_aly_crbh$crbh.pairs <- head(ath_aly_crbh$crbh.pairs)
ath_aly_crbh.kaks <- rbh2kaks(
    rbhpairs=ath_aly_crbh,
    cds1=ath,
    cds2=aly,
    model="Li")
head(ath_aly_crbh.kaks)
#>           aa1                   aa2 rbh_class Comp1 Comp2        seq1
#> 1 AT1G01040.1 Al_scaffold_0001_3256       rbh     1     7 AT1G01040.1
#> 2 AT1G01050.1  Al_scaffold_0001_128       rbh     2     8 AT1G01050.1
#> 3 AT1G01080.3  Al_scaffold_0001_125       rbh     3     9 AT1G01080.3
#> 4 AT1G01180.1  Al_scaffold_0001_114       rbh     4    10 AT1G01180.1
#> 5 AT1G01190.2 Al_scaffold_0001_4419       rbh     5    11 AT1G01190.2
#> 6 AT1G01260.3 Al_scaffold_0001_1326       rbh     6    12 AT1G01260.3
#>                    seq2                 ka                ks
#> 1 Al_scaffold_0001_3256   3.47214301182417          9.999999
#> 2  Al_scaffold_0001_128                  0 0.183183948635914
#> 3  Al_scaffold_0001_125 0.0790506471613155 0.163580204777153
#> 4  Al_scaffold_0001_114 0.0352750842763028 0.152463286123433
#> 5 Al_scaffold_0001_4419   1.92163132810055          9.999999
#> 6 Al_scaffold_0001_1326           9.999999          9.999999
#>                    vka                 vks                 Ka                Ks
#> 1     23.3505377395771            9.999999   3.47214301182417          9.999999
#> 2                    0 0.00302230749742857                  0 0.183183948635914
#> 3 0.000268905965208751 0.00195629182238787 0.0790506471613155 0.163580204777153
#> 4 0.000103935713186579 0.00124033104730168 0.0352750842763028 0.152463286123433
#> 5    0.197145150583422            9.999999   1.92163132810055          9.999999
#> 6             9.999999            9.999999           9.999999          9.999999
#>       Ka/Ks
#> 1 0.3472143
#> 2 0.0000000
#> 3 0.4832531
#> 4 0.2313677
#> 5 0.1921632
#> 6 1.0000000
## plot kaks
g.kaks <- plot_kaks(ath_aly_crbh.kaks)