ldest_comp  R Documentation 
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.
ldest_comp( ga, gb, K, pen = 1, useboot = TRUE, nboot = 50, se = TRUE, model = c("norm", "flex") )
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 ( 
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 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
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.