Multi-Locus Linkage Disequilibrium
LDscan computes a matrix of pairwise linkage disequilibrium (LD)
coefficients (|r|) 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.
LDscan(x, ...)
## S3 method for class 'DNAbin'
LDscan(x, quiet = FALSE, what = c("r", "Dprime"), ...)
## S3 method for class 'loci'
LDscan(x, depth = NULL, quiet = FALSE,
what = c("r", "Dprime"), ...)
LDmap(d, POS = NULL, breaks = NULL, col = NULL, border = NA,
angle = 0, asp = 1, cex = 1, scale.legend = 0.8, ...)x |
an object of class |
depth |
a vector of integers giving the the depth(s) (or lags) at which the r's are calculated. By default, all possible depths are considered. |
quiet |
a logical: should the progress of the operation be printed? |
what |
the quantity to be computed. Two choices are possible:
|
d |
a correlation matrix (can be an object of class |
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
|
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
|
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 methods ( |
The LD coefficient r 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 is not clear.
All levels of ploidy are accepted, but all loci should have the same ploidy level.
If depth is used, the r's are calculated only for the
pairs of loci that are distant by these values in x, but
necessarily on the chromosome. The returned list has names set with
the values of depth.
The value returned is actually |r| (not r^2).
LDscan returns an object of class "dist" by default, or
a list if depth is used.
Emmanuel Paradis
data(woodmouse)
d <- LDscan(woodmouse)
LDmap(d, seg.sites(woodmouse), seq(0, 1, .1))
## Not run:
## Download the VCF file from Dryad:
## https://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)
## LD map from the first 100 loci:
x <- read.vcf(fl, to = 100) # read only 100 loci
res <- LDscan(x)
bks <- seq(0, 1, 0.2)
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)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.