# Dprime: Get the standardized composite D'. In ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids

 Dprime R Documentation

## Get the standardized composite D'.

### Description

This function will either standardize by the maximum covariance conditional on the marginal genotype distribution, or by the maximum covariance conditional on the marginal allele frequencies.

### Usage

Dprime(qmat, type = c("allele", "geno"), constrain = FALSE)

### Arguments

 qmat The observed joint genotype distribution. type Should we condition on the marginal genotype distribution (type = "geno"), or should we condition on the allele frequency (type = "allele")? constrain A logical. This option is only applicable when type = "allele". Should return an value that is equal to D' under HWE (FALSE) or a value that is constrained to lie between -1 and 1 (TRUE)? Defaults to FALSE.

### Details

Note that when type = "allele" and constrain = FALSE, the resulting D' is constrained to fall between -K and K, where K is the ploidy of the species. However, under HWE, this measure is equal to haplotypic D'. Using constrain = TRUE will result in a measure that is constrained to lie between -1 and 1, but it will not equal haplotypic D' under HWE.

Using type = "geno" is its own thing and will not equal D' generally under HWE. When type = "geno", then the the constrain parameter has no effect.

### Value

A vector of length 2. The first element is the estimated D'. The second element is the normalization used.

David Gerard

### Examples

K <- 6
qmat <- matrix(stats::runif((K+1)^2), nrow = K+1)
qmat <- qmat / sum(qmat)
Dprime(qmat, type = "geno")
Dprime(qmat, type = "allele")

ldsep documentation built on Oct. 19, 2022, 1:08 a.m.