format_lddf: Format an element of 'mldest()' or 'sldest()' into an...

In ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids

Format an element of mldest() or sldest() into an upper-triangular matrix.

Description

Formats the LD estimates and standard errors output from running mldest() or sldest() into a more conventional upper-triangular matrix.

Usage

format_lddf(obj, element = "r2")

Arguments

obj	An object of class lddf, usually output from running either mldest() or sldest().
element	Which element in obj should we format into an upper-triangular matrix?

Value

A matrix of the selected elements. Only the upper-triangle of the matrix is filled. The lower-triangle and the diagonal are NA's.

Author(s)

David Gerard

Examples

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)

## Haplotypic LD estimates
lddf <- mldest(geno = genomat,
               K = K,
               nc = nc,
               type = "hap")

## Obtain the D estimates in matrix form
Dmat <- format_lddf(obj = lddf, element = "D")
Dmat

ldsep documentation built on Nov. 5, 2025, 6:25 p.m.