LDscan: Multi-Locus Linkage Disequilibrium

Description

LDscan computes a matrix of pairwise linkage disequilibrium (LD) coefficients (\(r^2\)) from a set of loci (which must be bi-allelic; if not, the results are not guaranteed to be meaningful). The genotypes must be phased.

LDmap plots a matrix of LD coefficients, optionally with the positions of the loci.

Usage

LDscan(x, quiet = FALSE)
LDmap(d, POS = NULL, breaks = NULL, col = NULL, border = NA,
      angle = 0, asp = 1, cex = 1, scale.legend = 0.8, ...)

Arguments

an object of class "loci" with phased genotypes.

quiet

a logical: should the progress of the operation be printed?

a correlation matrix (can be an object of class "dist").

POS

an optional vector of locus positions (e.g., from a VCF file; see examples).

breaks

a vector of break intervals to count the values in d; by default, ten equally-sized intervals are used.

col

an optional vector of colours; a scale from lightyellow to red is used by default.

border

the border of the rectangles: the default is to have no border (this is not the same than default in rect; see examples).

angle

value (in degrees) to rotate the graphic.

asp

the aspect ratio of the graphic; one by default so the elements are squares (not rectangles).

cex

the scaling of the labels and text.

scale.legend

the scaling of the legend rectangles.

…

further arguments passed to plot.default.

Value

an object of class "dist" for LDscan.

Details

The LD coefficient \(r^2\) is well defined when the two loci have only two alleles. In other cases, LD is well defined (see LD) but the definition of \(r^2\) is not clear.

All levels of ploidy are accepted, but all loci should have the same ploidy level.

Examples

Run this code

# NOT RUN {
## Download the VCF file from Dryad:
## http://dx.doi.org/10.5061/dryad.446sv.2

## the VCF file should have this name:
fl <- "global.pop.GATK.SNP.hard.filters.V3.phased_all.pop.maf.05.recode.vcf.gz"

info.fly <- VCFloci(fl)

bks <- seq(0, 1, 0.2)

## LD map from the first 100 loci:
x <- read.vcf(fl, to = 100) # read only 100 loci
res <- LDscan(x)
LDmap(res, info.fly$POS[1:100], bks, scale.legend = 3)

## check the chromosomes:
table(info.fly$CHROM)

## LD map from 100 loci randomly distributed on the chromosome:
s <- ceiling(seq(1, 224253, length.out = 100))
xs <- read.vcf(fl, which.loci = s)
res2 <- LDscan(xs)
LDmap(res2, info.fly$POS[s], bks, scale.legend = 3)

## something simpler with 10 loci:
x10 <- x[, 1:10]
## the VCF file has no locus IDs, so we give some here:
names(x10) <- paste0("Loc", 1:10)
res10 <- LDscan(x10, quiet = TRUE)
LDmap(res10, angle = 45, border = NULL)
# }