ldest_comp {ldsep} | R Documentation |
Estimates of composite pairwise LD based either on genotype estimates or genotype likelihoods.
Description
This function will estimate the composite LD between two loci, either using genotype estimates or using genotype likelihoods. The resulting measures of LD are generalizations of Burrow's "composite" LD measure.
Usage
ldest_comp(
ga,
gb,
K,
pen = 1,
useboot = TRUE,
nboot = 50,
se = TRUE,
model = c("norm", "flex")
)
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. |
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 |
useboot |
Should we use bootstrap standard errors |
nboot |
The number of bootstrap iterations to use is
|
se |
A logical. Should we calculate standard errors ( |
model |
Should we assume the class of joint genotype distributions
is from the proportional bivariate normal ( |
Value
A vector with some or all of the following elements:
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 Fisher-z transformation of
r
.z_se
The standard error of the Fisher-z 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.
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)
## Composite LD with genotypes
ldout1 <- ldest_comp(ga = ga,
gb = gb,
K = K)
head(ldout1)
## Composite LD with genotype likelihoods
ldout2 <- ldest_comp(ga = gamat,
gb = gbmat,
K = K,
se = FALSE,
model = "flex")
head(ldout2)
## Composite LD with genotype likelihoods and proportional bivariate normal
ldout3 <- ldest_comp(ga = gamat,
gb = gbmat,
K = K,
model = "norm")
head(ldout3)