gl.ld.distance {dartR.popgen}

Plots linkage disequilibrium against distance by population disequilibrium patterns

Description

The function creates a plot showing the pairwise LD measure against distance in number of base pairs pooled over all the chromosomes and a red line representing the threshold (R.squared = 0.2) that is commonly used to imply that two loci are unlinked (Delourme et al., 2013; Li et al., 2014).

Usage

gl.ld.distance(
  ld.report,
  ld.resolution = 1e+05,
  pop.colors = NULL,
  plot.title = " ",
  plot.theme = NULL,
  plot.out = TRUE,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

Arguments

ld.report

Output from function gl.report.ld.map [required].

ld.resolution

Resolution at which LD should be reported in number of base pairs [default NULL].

pop.colors

A color palette for box plots by population or a list with as many colors as there are populations in the dataset [default NULL].

plot.title

Title of tyh plot [default " "].

plot.theme

User specified theme [default NULL].

plot.out

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

plot.file

Name for the RDS binary file to save (base name only, exclude extension) [default NULL]

plot.dir

Directory in which to save files [default = working directory]

verbose

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

Value

A dataframe with information of LD against distance by population.

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

References

• Delourme, R., Falentin, C., Fomeju, B. F., Boillot, M., Lassalle, G., André, I., . . . Marty, A. (2013). High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napusL. BMC genomics, 14(1), 120.

• Li, X., Han, Y., Wei, Y., Acharya, A., Farmer, A. D., Ho, J., . . . Brummer, E. C. (2014). Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium. PLoS One, 9(1), e84329.

See Also

Other ld functions: gl.ld.haplotype()

Examples

if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) {
  require("dartR.data")
  x <- platypus.gl
  x <- gl.filter.callrate(x, threshold = 1)
  x <- gl.filter.monomorphs(x)
  x$position <- x$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
  x$chromosome <- as.factor(x$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1)
  ld_res <- gl.report.ld.map(x, ld.max.pairwise = 10000000)
  ld_res_2 <- gl.ld.distance(ld_res, ld.resolution = 1000000)
}