Reports summary of base pair frequencies

This script calculates the frequencies of the four DNA nucleotide bases: adenine (A), cytosine (C), 'guanine (G) and thymine (T), and the frequency of transitions (Ts) and transversions (Tv) in a DArT genlight object.

Usage

gl.report.bases(
  x,
  plot.out = TRUE,
  plot_theme = theme_dartR(),
  plot_colors = two_colors,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].

plot.out

If TRUE, histograms of base composition are produced [default TRUE].

plot_theme

Theme for the plot. See Details for options [default theme_dartR()].

plot_colors

List of two color names for the borders and fill of the plots [default two_colors].

save2tmp

If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity]

Value

The unchanged genlight object

Details

The script checks first if trimmed sequences are included in the locus metadata (@other$loc.metrics$TrimmedSequence), and if so, tallies up the numbers of A, T, G and C bases. Only the reference state at the SNP locus is counted. Counts of transitions (Ts) and transversions (Tv) assume that there is no directionality, that is C->T is the same as T->C, because the reference state is arbitrary.

For presence/absence data (SilicoDArT), it is not possible to count transversions or transitions or transversions/transitions ratio because the SNP data is not available, only a single sequence tag.

Examples of other themes that can be used can be consulted in

• https://ggplot2.tidyverse.org/reference/ggtheme.html and

• https://yutannihilation.github.io/allYourFigureAreBelongToUs/ggthemes/

See also

Other report functions: gl.report.callrate(), gl.report.diversity(), gl.report.hamming(), gl.report.heterozygosity(), gl.report.hwe(), gl.report.ld.map(), gl.report.locmetric(), gl.report.maf(), gl.report.monomorphs(), gl.report.overshoot(), gl.report.parent.offspring(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.sexlinked(), gl.report.taglength()

Author

Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr

Examples

# SNP data
  out <- gl.report.bases(testset.gl)
#> Starting gl.report.bases 
#>   Processing genlight object with SNP data
#>   Counting the bases
#>   Counting Transitions and Transversions
#>   Average trimmed sequence length: 60.7 ( 20 to 69 ) 
#>   Total number of trimmed sequences: 255 
#>   Base frequencies (%)
#>     A: 25.01 
#>     G: 26.67 
#>     T: 24.12 
#>     C: 24.2 
#> 
#>   Transitions  : 65.49 
#>   Transversions: 34.51 
#>   tv/ts ratio: 1.8977 
#> 

#>   Returning a list containing
#> [[1]] $freq -- the table of base frequencies and transition/transversion ratios;
#> [[2]] $plotbases -- ggplot bargraph of base frequencies;
#> [[3]] $plottstv -- ggplot bargraph of transitions and transversions.Completed: gl.report.bases 
#> 
  #' # Tag P/A data
  out <- gl.report.bases(testset.gs)
#> Starting gl.report.bases 
#>   Processing genlight object with Presence/Absence (SilicoDArT) data
#>   Counting the bases
#>   Average trimmed sequence length: 63.6 ( 29 to 69 ) 
#>   Total number of trimmed sequences: 255 
#>   Base frequencies (%)
#>     A: 27.79 
#>     G: 23.93 
#>     T: 26.94 
#>     C: 21.34 
#> 
#>   Tag P/A data (SilicoDArT), transition/transversions 
#>                     cannot be calculated
#> 

#>   Returning a list containing
#> [[1]] $freq -- the table of base frequencies and transition/transversion ratios;
#> [[2]] $plotbases -- ggplot bargraph of base frequencies;
#> [[3]] $plottstv -- ggplot bargraph of transitions and transversions.Completed: gl.report.bases 
#>