Compute LD Scores

Compute LD scores from an LD reference, optionally stratified by annotations.

Usage

computeLdScores(ldRef, annotations = NULL, ...)

# S4 method for class 'LdEigen'
computeLdScores(ldRef, annotations = NULL, ...)

# S4 method for class 'LdScore'
computeLdScores(ldRef, annotations = NULL, ...)

Arguments

ldRef

An LdStatistic object.

annotations

An AnnotationMatrix object, or NULL.

...

Additional arguments.

Value

A numeric matrix of LD scores (SNPs x annotations+1).

Examples

data(ldEigenExample)
computeLdScores(ldEigenExample)
#>       base_l2
#>  [1,]    1.81
#>  [2,]    1.81
#>  [3,]    1.81
#>  [4,]    1.81
#>  [5,]    1.81
#>  [6,]    1.81
#>  [7,]    1.81
#>  [8,]    1.81
#>  [9,]    1.81
#> [10,]    1.81
#> [11,]    1.81
#> [12,]    1.81
#> [13,]    1.81
#> [14,]    1.81
#> [15,]    1.81
#> [16,]    1.81
#> [17,]    1.81
#> [18,]    1.81
#> [19,]    1.81
#> [20,]    1.81