Convert H2Estimate to S-LDSC Trait Format — h2EstimateToSldscTrait • pecotmr

Convert an H2Estimate object into the list format expected by standardizeSldscTrait and metaSldscRandom. This bridges the h2 estimation methods (LDER, gLDSC, HDL) into the sldscWrapper.R postprocessing pipeline.

Usage

h2EstimateToSldscTrait(h2Est)

Arguments

h2Est: An H2Estimate object with enrichment and tauBlocks.

Value

A named list matching the format of readSldscTrait:

categories: Character vector of annotation names
tau: Named numeric vector of per-annotation coefficients
tauSe: Named numeric vector of tau standard errors
enrichment: Named numeric vector of enrichment ratios
enrichmentSe: Named numeric vector of enrichment SEs
enrichmentP: Named numeric vector of enrichment p-values
propH2: Named numeric vector of proportion of h2
propSnps: Named numeric vector of proportion of SNPs
h2g: Numeric scalar, global h2 estimate
tauBlocks: Matrix (nBlocks x nCategories) for jackknife
nBlocks: Integer, number of jackknife blocks

Examples

data(h2EstimateExample)
h2EstimateToSldscTrait(h2EstimateExample)
#> $categories
#> [1] "annot1" "annot2"
#> 
#> $tau
#> annot1 annot2 
#>  1e-07  2e-07 
#> 
#> $tauSe
#> annot1 annot2 
#>  5e-08  6e-08 
#> 
#> $enrichment
#> annot1 annot2 
#>      2      3 
#> 
#> $enrichmentSe
#> annot1 annot2 
#>    0.5    0.7 
#> 
#> $enrichmentP
#> annot1 annot2 
#>  0.010  0.001 
#> 
#> $propH2
#> annot1 annot2 
#>    0.3    0.5 
#> 
#> $propSnps
#> annot1 annot2 
#>   0.15   0.17 
#> 
#> $h2g
#> [1] 0.3
#> 
#> $tauBlocks
#>             annot1      annot2
#>  [1,]  0.120139084 -0.04891095
#>  [2,] -1.812376850 -0.84323377
#>  [3,]  0.151582984 -2.07527077
#>  [4,] -1.119221005 -0.36076315
#>  [5,]  0.001908206 -0.63768966
#>  [6,]  1.188518494 -0.36627803
#>  [7,] -0.505343855  2.35536390
#>  [8,] -0.099234393  1.09337723
#>  [9,]  0.305353199  0.28584100
#> [10,]  0.198409703  0.99365778
#> 
#> $nBlocks
#> [1] 10
#>