Reports minor allele frequency (MAF) for each locus in a SNP dataset

This script provides summary histograms of MAF for each population in the dataset and an overall histogram to assist the decision of choosing thresholds for the filter function gl.filter.maf

Usage

gl.report.maf(
  x,
  maf.limit = 0.5,
  ind.limit = 5,
  plot.out = TRUE,
  plot_theme = theme_dartR(),
  plot_colors_pop = discrete_palette,
  plot_colors_all = two_colors,
  bins = 25,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data [required].

maf.limit

Show histograms MAF range <= maf.limit [default 0.5].

ind.limit

Show histograms only for populations of size greater than ind.limit [default 5].

plot.out

Specify if plot is to be produced [default TRUE].

plot_theme

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

plot_colors_pop

A color palette for population plots [default discrete_palette].

plot_colors_all

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

bins

Number of bins to display in histograms [default 25].

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

An unaltered genlight object

Details

The function gl.filter.maf will filter out the loci with MAF below a specified threshold.

Function's output

The minimum, maximum, mean and a tabulation of MAF quantiles against thresholds rate are provided. Output also includes a boxplot and a histogram.

This function reports the MAF for each of several quantiles. Quantiles are partitions of a finite set of values into q subsets of (nearly) equal sizes. In this function q = 20. Quantiles are useful measures because they are less susceptible to long-tailed distributions and outliers.

Plots and table are saved to the temporal directory (tempdir) and can be accessed with the function gl.print.reports and listed with the function gl.list.reports. Note that they can be accessed only in the current R session because tempdir is cleared each time that the R session is closed.

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

gl.filter.maf, gl.list.reports, gl.print.reports

Other report functions: gl.report.bases(), gl.report.callrate(), gl.report.diversity(), gl.report.hamming(), gl.report.heterozygosity(), gl.report.hwe(), gl.report.ld.map(), gl.report.locmetric(), gl.report.monomorphs(), gl.report.overshoot(), gl.report.pa(), gl.report.parent.offspring(), 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

gl <- gl.report.maf(platypus.gl)
#> Starting gl.report.maf 
#>   Processing genlight object with SNP data
#>   Warning: data include loci that are scored NA across all individuals.
#>   Consider filtering using gl <- gl.filter.allna(gl)
#> Starting gl.report.maf 
#> 
#>   Reporting Minor Allele Frequency (MAF) by Locus
#>   No. of loci = 1000 
#>   No. of individuals = 81 
#>     Minimum      :  0.00617284 
#>     1st quantile :  0.03797468 
#>     Median       :  0.1125 
#>     Mean         :  0.1589901 
#>     3r quantile  :  0.2531646 
#>     Maximum      :  0.5 
#>     Missing Rate Overall:  0.07 
#> 

#>    Quantile  Threshold Retained Percent Filtered Percent
#> 1      100% 0.50000000        1     0.2      640    99.8
#> 2       95% 0.44444444       34     5.3      607    94.7
#> 3       90% 0.39102564       65    10.1      576    89.9
#> 4       85% 0.34375000       97    15.1      544    84.9
#> 5       80% 0.29375000      129    20.1      512    79.9
#> 6       75% 0.25316456      161    25.1      480    74.9
#> 7       70% 0.21875000      193    30.1      448    69.9
#> 8       65% 0.18750000      225    35.1      416    64.9
#> 9       60% 0.16049383      257    40.1      384    59.9
#> 10      55% 0.13580247      292    45.6      349    54.4
#> 11      50% 0.11250000      322    50.2      319    49.8
#> 12      45% 0.09259259      360    56.2      281    43.8
#> 13      40% 0.08024691      392    61.2      249    38.8
#> 14      35% 0.06250000      418    65.2      223    34.8
#> 15      30% 0.05000000      450    70.2      191    29.8
#> 16      25% 0.03797468      481    75.0      160    25.0
#> 17      20% 0.03086420      513    80.0      128    20.0
#> 18      15% 0.01851852      554    86.4       87    13.6
#> 19      10% 0.01234568      585    91.3       56     8.7
#> 20       5% 0.00625000      610    95.2       31     4.8
#> 21       0% 0.00617284      641   100.0        0     0.0
#> Completed: gl.report.maf 
#>