mldest  R Documentation 
This function is a wrapper to run ldest()
for many pairs of
SNPs. This takes a maximum likelihood approach to LD estimation. See
ldfast()
for a methodofmoments approach to LD estimation.
Support is provided for parallelization through the foreach and doParallel
packages. See Gerard (2021) for details.
mldest( geno, K, nc = 1, type = c("hap", "comp"), model = c("norm", "flex"), pen = ifelse(type == "hap", 2, 1), se = TRUE )
geno 
One of two possible inputs:

K 
The ploidy of the species. Assumed to be the same for all individuals. 
nc 
The number of computing cores to use. This should never be
more than the number of cores available in your computing environment.
You can determine the maximum number of available cores by running

type 
The type of LD to calculate. The available types are
haplotypic LD ( 
model 
When 
pen 
The penalty to be applied to the likelihood. You can think about
this as the prior sample size. Should be greater than 1. Does not
apply if 
se 
A logical. Should we calculate standard errors ( 
See ldest()
for details on the different types of LD
estimators supported.
A data frame of class c("lddf", "data.frame")
with some or all of the following elements:
i
The index of the first SNP.
j
The index of the second SNP.
snpi
The row name corresponding to SNP i
, if
row names are provided.
snpj
The row name corresponding to SNP j
, if
row names are provided.
D
The estimate of the LD coefficient.
D_se
The standard error of the estimate of the LD coefficient.
r2
The estimate of the squared Pearson correlation.
r2_se
The standard error of the estimate of the squared Pearson correlation.
r
The estimate of the Pearson correlation.
r_se
The standard error of the estimate of the Pearson correlation.
Dprime
The estimate of the standardized LD
coefficient. When type
= "comp", this corresponds
to the standardization where we fix allele frequencies.
Dprime_se
The standard error of Dprime
.
Dprimeg
The estimate of the standardized LD coefficient. This corresponds to the standardization where we fix genotype frequencies.
Dprimeg_se
The standard error of Dprimeg
.
z
The Fisherz transformation of r
.
z_se
The standard error of the Fisherz
transformation of r
.
p_ab
The estimated haplotype frequency of ab. Only returned if estimating the haplotypic LD.
p_Ab
The estimated haplotype frequency of Ab. Only returned if estimating the haplotypic LD.
p_aB
The estimated haplotype frequency of aB. Only returned if estimating the haplotypic LD.
p_AB
The estimated haplotype frequency of AB. Only returned if estimating the haplotypic LD.
q_ij
The estimated frequency of genotype i at locus 1 and genotype j at locus 2. Only returned if estimating the composite LD.
n
The number of individuals used to estimate pairwise LD.
David Gerard
Gerard, David. "Pairwise Linkage Disequilibrium Estimation for Polyploids." Molecular Ecology Resources 21, no. 4 (2021): 12301242. doi: 10.1111/17550998.13349
ldfast()
Fast, momentbased approach to LD estimation that also accounts for genotype uncertainty.
ldest()
For the base function that estimates pairwise LD.
sldest()
For estimating pairwise LD along a sliding window.
format_lddf()
For formatting the output of
mldest()
as a matrix.
plot.lddf()
For plotting the output of
mldest()
.
set.seed(1) ## Simulate genotypes when true correlation is 0 nloci < 5 nind < 100 K < 6 nc < 1 genomat < matrix(sample(0:K, nind * nloci, TRUE), nrow = nloci) ## Composite LD estimates lddf < mldest(geno = genomat, K = K, nc = nc, type = "comp") lddf[1:6, 1:6]
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