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

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

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

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
#>    1         2          3            4           5
#> 1 NA -0.015268 0.01127912 -0.004729285 -0.02260301
#> 2 NA        NA 0.00394976  0.009062196 -0.02153841
#> 3 NA        NA         NA  0.023425711 -0.01808722
#> 4 NA        NA         NA           NA -0.01764326
#> 5 NA        NA         NA           NA          NA