ldest_hap: Estimate haplotypic pair-wise LD using either genotypes or...
In ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids
ldest_hap R Documentation
Estimate haplotypic pair-wise LD using either genotypes or genotype
likelihoods.
Description
Given genotype (allele dosage) or genotype likelihood data
for each individual at a pair of loci, this function will
calculate the maximum likelihood estimates
and their corresponding asymptotic standard errors of some
measures of linkage disequilibrium (LD): D, D', the Pearson correlation,
the squared Pearson correlation, and the Fisher-z transformation of the
Pearson correlation. This function can be used for both
diploids and polyploids.
Usage
ldest_hap(
ga,
gb,
K,
reltol = 10^-8,
nboot = 100,
useboot = FALSE,
pen = 2,
grid_init = FALSE,
se = TRUE
)
Arguments
ga
One of two possible inputs:
A vector of counts, containing the genotypes for each
individual at the first locus. When type = "comp",
the vector of genotypes may be continuous (e.g. the
posterior mean genotype).
A matrix of genotype log-likelihoods at the first locus.
The rows index the individuals and the columns index
the genotypes. That is ga[i, j] is the genotype
likelihood of individual i for genotype j-1.
gb
One of two possible inputs:
A vector of counts, containing the genotypes for each
individual at the second locus. When type = "comp",
the vector of genotypes may be continuous (e.g. the
posterior mean genotype).
A matrix of genotype log-likelihoods at the second locus.
The rows index the individuals and the columns index
the genotypes. That is gb[i, j] is the genotype
likelihood of individual i for genotype j-1.
K
The ploidy of the species. Assumed to be the same for all
individuals.
reltol
The relative tolerance for the stopping criterion.
nboot
Sometimes, the MLE standard errors don't exist. So we use
the bootstrap as a backup. nboot specifies the number
of bootstrap iterations.
useboot
A logical. Optionally, you may always use the bootstrap
to estimate the standard errors (TRUE). These will be more
accurate but also much slower, so this defaults to FALSE. Only
applicable if using genotype likelihoods.
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 model = "norm", type = "comp", and using
genotype likelihoods. Also does not apply when type = "comp"
and using genotypes.
grid_init
A logical. Should we initialize the gradient ascent
at a grid of initial values (TRUE) or just initialize
at one value corresponding to the simplex point
rep(0.25, 4) (FALSE)?
se
A logical. Should we calculate standard errors (TRUE) or
not (FALSE). Calculating standard errors can be really slow
when type = "comp", model = "flex", and when using
genotype likelihoods. Otherwise, standard error calculations
should be pretty fast.
Details
Let A and a be the reference and alternative alleles, respectively, at
locus 1. Let B and b be the reference and alternative alleles,
respectively, at locus 2. Let paa, pAb, paB, and pAB be the
frequencies of haplotypes ab, Ab, aB, and AB, respectively.
Let pA = pAb + pAB and let pB = paB + pAB
The ldest returns estimates of the following measures
of LD.
D: pAB - pA pB
D': D / Dmax, where Dmax = min(pA pB, (1 - pA) (1 - pB)) if
D < 0 and Dmax = min(pA (1 - pB), pA (1 - pB)) if D > 0
r-squared: The squared Pearson correlation,
r^2 = D^2 / (pA (1 - pA) pB (1 - pB))
r: The Pearson correlation,
r = D / sqrt(pA (1 - pA) pB (1 - pB))
Estimates are obtained via maximum likelihood under the assumption
of Hardy-Weinberg equilibrium. The likelihood is calculated by
integrating over the possible haplotypes for each pair of genotypes.
The resulting standard errors are based on the square roots of the inverse of the
negative Fisher-information. This is from standard maximum likelihood
theory. The Fisher-information is known to be biased low, so the actual
standard errors are probably a little bigger for small n (n < 20).
In some cases the Fisher-information matrix is singular, and so we
in these cases we return a bootstrap estimate of the standard error.
The standard error estimate of the squared Pearson correlation is not
valid when r^2 = 0.
In cases where either SNP is estimated to be monoallelic
(pA %in% c(0, 1) or pB %in% c(0, 1)), this function
will return LD estimates of NA.
Value
A vector with some or all of the following elements:
DThe estimate of the LD coefficient.
D_seThe standard error of the estimate of
the LD coefficient.
r2The estimate of the squared Pearson correlation.
r2_seThe standard error of the estimate of the
squared Pearson correlation.
rThe estimate of the Pearson correlation.
r_seThe standard error of the estimate of the
Pearson correlation.
DprimeThe estimate of the standardized LD
coefficient. When type = "comp", this corresponds
to the standardization where we fix allele frequencies.
Dprime_seThe standard error of Dprime.
DprimegThe estimate of the standardized LD
coefficient. This corresponds to the standardization where
we fix genotype frequencies.
Dprimeg_seThe standard error of Dprimeg.
zThe Fisher-z transformation of r.
z_seThe standard error of the Fisher-z
transformation of r.
p_abThe estimated haplotype frequency of ab.
Only returned if estimating the haplotypic LD.
p_AbThe estimated haplotype frequency of Ab.
Only returned if estimating the haplotypic LD.
p_aBThe estimated haplotype frequency of aB.
Only returned if estimating the haplotypic LD.
p_ABThe estimated haplotype frequency of AB.
Only returned if estimating the haplotypic LD.
q_ijThe estimated frequency of genotype i at locus 1
and genotype j at locus 2. Only returned if estimating the
composite LD.
nThe number of individuals used to estimate pairwise LD.
Author(s)
David Gerard
Examples
set.seed(1)
n <- 100 # sample size
K <- 6 # ploidy
## generate some fake genotypes when LD = 0.
ga <- stats::rbinom(n = n, size = K, prob = 0.5)
gb <- stats::rbinom(n = n, size = K, prob = 0.5)
head(ga)
head(gb)
## generate some fake genotype likelihoods when LD = 0.
gamat <- t(sapply(ga, stats::dnorm, x = 0:K, sd = 1, log = TRUE))
gbmat <- t(sapply(gb, stats::dnorm, x = 0:K, sd = 1, log = TRUE))
head(gamat)
head(gbmat)
## Haplotypic LD with genotypes
ldout1 <- ldest_hap(ga = ga,
gb = gb,
K = K)
head(ldout1)
## Haplotypic LD with genotype likelihoods
ldout2 <- ldest_hap(ga = gamat,
gb = gbmat,
K = K)
head(ldout2)
ldsep documentation built on Nov. 5, 2025, 6:25 p.m.
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| ldest_hap | R Documentation |
Estimate haplotypic pair-wise LD using either genotypes or genotype likelihoods.
Description
Given genotype (allele dosage) or genotype likelihood data for each individual at a pair of loci, this function will calculate the maximum likelihood estimates and their corresponding asymptotic standard errors of some measures of linkage disequilibrium (LD): D, D', the Pearson correlation, the squared Pearson correlation, and the Fisher-z transformation of the Pearson correlation. This function can be used for both diploids and polyploids.
Usage
ldest_hap(
ga,
gb,
K,
reltol = 10^-8,
nboot = 100,
useboot = FALSE,
pen = 2,
grid_init = FALSE,
se = TRUE
)
Arguments
ga |
One of two possible inputs:
|
gb |
One of two possible inputs:
|
K |
The ploidy of the species. Assumed to be the same for all individuals. |
reltol |
The relative tolerance for the stopping criterion. |
nboot |
Sometimes, the MLE standard errors don't exist. So we use
the bootstrap as a backup. |
useboot |
A logical. Optionally, you may always use the bootstrap
to estimate the standard errors ( |
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 |
grid_init |
A logical. Should we initialize the gradient ascent
at a grid of initial values ( |
se |
A logical. Should we calculate standard errors ( |
Details
Let A and a be the reference and alternative alleles, respectively, at
locus 1. Let B and b be the reference and alternative alleles,
respectively, at locus 2. Let paa, pAb, paB, and pAB be the
frequencies of haplotypes ab, Ab, aB, and AB, respectively.
Let pA = pAb + pAB and let pB = paB + pAB
The ldest returns estimates of the following measures
of LD.
D: pAB - pA pB
D': D / Dmax, where Dmax = min(pA pB, (1 - pA) (1 - pB)) if D < 0 and Dmax = min(pA (1 - pB), pA (1 - pB)) if D > 0
r-squared: The squared Pearson correlation, r^2 = D^2 / (pA (1 - pA) pB (1 - pB))
r: The Pearson correlation, r = D / sqrt(pA (1 - pA) pB (1 - pB))
Estimates are obtained via maximum likelihood under the assumption of Hardy-Weinberg equilibrium. The likelihood is calculated by integrating over the possible haplotypes for each pair of genotypes.
The resulting standard errors are based on the square roots of the inverse of the negative Fisher-information. This is from standard maximum likelihood theory. The Fisher-information is known to be biased low, so the actual standard errors are probably a little bigger for small n (n < 20). In some cases the Fisher-information matrix is singular, and so we in these cases we return a bootstrap estimate of the standard error.
The standard error estimate of the squared Pearson correlation is not valid when r^2 = 0.
In cases where either SNP is estimated to be monoallelic
(pA %in% c(0, 1) or pB %in% c(0, 1)), this function
will return LD estimates of NA.
Value
A vector with some or all of the following elements:
DThe estimate of the LD coefficient.
D_seThe standard error of the estimate of the LD coefficient.
r2The estimate of the squared Pearson correlation.
r2_seThe standard error of the estimate of the squared Pearson correlation.
rThe estimate of the Pearson correlation.
r_seThe standard error of the estimate of the Pearson correlation.
DprimeThe estimate of the standardized LD coefficient. When
type= "comp", this corresponds to the standardization where we fix allele frequencies.Dprime_seThe standard error of
Dprime.DprimegThe estimate of the standardized LD coefficient. This corresponds to the standardization where we fix genotype frequencies.
Dprimeg_seThe standard error of
Dprimeg.zThe Fisher-z transformation of
r.z_seThe standard error of the Fisher-z transformation of
r.p_abThe estimated haplotype frequency of ab. Only returned if estimating the haplotypic LD.
p_AbThe estimated haplotype frequency of Ab. Only returned if estimating the haplotypic LD.
p_aBThe estimated haplotype frequency of aB. Only returned if estimating the haplotypic LD.
p_ABThe estimated haplotype frequency of AB. Only returned if estimating the haplotypic LD.
q_ijThe estimated frequency of genotype i at locus 1 and genotype j at locus 2. Only returned if estimating the composite LD.
nThe number of individuals used to estimate pairwise LD.
Author(s)
David Gerard
Examples
set.seed(1)
n <- 100 # sample size
K <- 6 # ploidy
## generate some fake genotypes when LD = 0.
ga <- stats::rbinom(n = n, size = K, prob = 0.5)
gb <- stats::rbinom(n = n, size = K, prob = 0.5)
head(ga)
head(gb)
## generate some fake genotype likelihoods when LD = 0.
gamat <- t(sapply(ga, stats::dnorm, x = 0:K, sd = 1, log = TRUE))
gbmat <- t(sapply(gb, stats::dnorm, x = 0:K, sd = 1, log = TRUE))
head(gamat)
head(gbmat)
## Haplotypic LD with genotypes
ldout1 <- ldest_hap(ga = ga,
gb = gb,
K = K)
head(ldout1)
## Haplotypic LD with genotype likelihoods
ldout2 <- ldest_hap(ga = gamat,
gb = gbmat,
K = K)
head(ldout2)
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