LDscan | R Documentation |
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 |
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
LD
, read.vcf
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.