| gl.report.ld.map {dartR.base} | R Documentation |
Calculates pairwise linkage disequilibrium by population
Description
This function calculates pairwise linkage disequilibrium (LD) by population
using the function ld (package snpStats).
If SNPs are not mapped to a reference genome, the parameter
ld.max.pairwise
should be set as NULL (the default). In this case, the
function will assign the same chromosome ("1") to all the SNPs in the dataset
and assign a sequence from 1 to n loci as the position of each SNP. The
function will then calculate LD for all possible SNP pair combinations.
If SNPs are mapped to a reference genome, the parameter
ld.max.pairwise
should be filled out (i.e. not NULL). In this case, the
information for SNP's position should be stored in the genlight accessor
"@position" and the SNP's chromosome name in the accessor "@chromosome"
(see examples). The function will then calculate LD within each chromosome
and for all possible SNP pair combinations within a distance of
ld.max.pairwise.
Usage
gl.report.ld.map(
x,
ld.max.pairwise = NULL,
maf = 0.05,
ld.stat = "R.squared",
ind.limit = 10,
stat.keep = "AvgPIC",
ld.threshold.pops = 0.2,
plot.display = TRUE,
plot.theme = theme_dartR(),
plot.file = NULL,
plot.dir = NULL,
histogram.colors = NULL,
boxplot.colors = NULL,
bins = 50,
verbose = NULL
)
Arguments
x |
Name of the genlight object containing the SNP data [required]. |
ld.max.pairwise |
Maximum distance in number of base pairs at which LD should be calculated [default NULL]. |
maf |
Minor allele frequency (by population) threshold to filter out loci. If a value > 1 is provided it will be interpreted as MAC (i.e. the minimum number of times an allele needs to be observed) [default 0.05]. |
ld.stat |
The LD measure to be calculated: "LLR", "OR", "Q", "Covar",
"D.prime", "R.squared", and "R". See |
ind.limit |
Minimum number of individuals that a population should contain to take it in account to report loci in LD [default 10]. |
stat.keep |
Name of the column from the slot |
ld.threshold.pops |
LD threshold to report in the plot of "Number of populations in which the same SNP pair are in LD" [default 0.2]. |
plot.display |
If TRUE, histograms of base composition are displayed in the plot window [default TRUE]. |
plot.theme |
Theme for the plot. See Details for options [default theme_dartR()]. |
plot.file |
Name for the RDS binary file to save (base name only, exclude extension) [default NULL] |
plot.dir |
Directory to save the plot RDS files [default as specified by the global working directory or tempdir()] |
histogram.colors |
Vector with two color names for the borders and fill [default NULL]. |
boxplot.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]. |
bins |
Number of bins to display in histograms [default 50]. |
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]. |
Details
This function reports LD between SNP pairs by population.
The function gl.filter.ld filters out the SNPs in LD using as
input the results of gl.report.ld.map. The actual number of
SNPs to be filtered out depends on the parameters set in the function
gl.filter.ld.
Boxplots of LD by population and
a histogram showing LD frequency are presented.
Value
A dataframe with information for each SNP pair in LD.
Author(s)
Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr
See Also
Other graphics:
gl.colors(),
gl.map.interactive(),
gl.plot.heatmap(),
gl.select.colors(),
gl.select.shapes(),
gl.smearplot(),
gl.tree.nj()
Examples
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)