Kriging-style LD-consistency outlier QC

Flags variants whose observed z-score is inconsistent with the value predicted from its LD neighbours, using susieR's kriging diagnostic. susieR::kriging_rss() computes the leave-one-out conditional distribution of each z_i given the rest (with the LD-mismatch scale s defaulting to susieR::estimate_s_rss()) and a per-variant logLR for the allele-switch hypothesis. This helper reuses susieR's own allele-switch rule — logLR > logLRThreshold & abs(z) > zThreshold (the same logLR > 2 & |z| > 2 used in susie_rss_utils) — to flag variants whose sign should be flipped. RSS-only helper, opt-in via alleleFlipKriging; never wired into alleleQc() / matchRefPanel(). Requires a susieR that provides kriging_rss() and estimate_s_rss().

Usage

krigingOutlierQc(
  zScore,
  R,
  n,
  variantIds = NULL,
  zThreshold = 2,
  logLRThreshold = 2
)

Arguments

zScore

Numeric vector of harmonized z-scores.

R

Square LD correlation matrix aligned to zScore.

n

Sample size, forwarded to susieR::kriging_rss() (whose default s is susieR::estimate_s_rss()).

variantIds

Optional variant IDs for the diagnostics table.

zThreshold

Absolute-z cutoff for the allele-switch rule (default 2, matching susieR).

logLRThreshold

Log-likelihood-ratio cutoff for the allele-switch rule (default 2, matching susieR).

Value

A list with flip (logical vector; TRUE = allele switch, z-score should be sign-flipped) and diagnostics (data frame of per-variant z, condmean, z_std_diff, logLR, and the flipped flag).

Examples

data(eqtlRegionExample)
X <- eqtlRegionExample$X[, 1:20]
R <- cor(X)
krigingOutlierQc(
  zScore = rnorm(20), R = R, n = 415, variantIds = colnames(X))
#> $flip
#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 
#> $diagnostics
#> # A tibble: 20 × 6
#>    variant_id               z condmean z_std_diff     logLR flipped
#>    <chr>                <dbl>    <dbl>      <dbl>     <dbl> <lgl>  
#>  1 chr22:32119788:T:C  0.596  -4.61e-8     0.597   7.19e- 8 FALSE  
#>  2 chr22:32119867:T:G -0.0394 -2.17e-8    -0.0394 -2.23e- 9 FALSE  
#>  3 chr22:32119961:T:G -0.662   6.84e-8    -0.662   1.18e- 7 FALSE  
#>  4 chr22:32120053:T:C  0.361   2.35e-8     0.361  -2.22e- 8 FALSE  
#>  5 chr22:32120593:A:G -0.263   4.75e-8    -0.264   3.27e- 8 FALSE  
#>  6 chr22:32120636:T:C -0.772  -1.53e-8    -0.772  -3.08e- 8 FALSE  
#>  7 chr22:32120932:G:A  1.81   -3.96e-8     1.81    1.87e- 7 FALSE  
#>  8 chr22:32120975:A:G -0.585  -4.37e-8    -0.585  -6.69e- 8 FALSE  
#>  9 chr22:32121290:C:T -1.47   -2.18e-8    -1.46   -8.33e- 8 FALSE  
#> 10 chr22:32121498:A:C -1.99   -1.98e-9    -1.98   -1.03e- 8 FALSE  
#> 11 chr22:32121635:T:G -0.802   6.72e-8    -0.802   1.41e- 7 FALSE  
#> 12 chr22:32121702:A:G -0.423   3.44e-8    -0.424   3.81e- 8 FALSE  
#> 13 chr22:32121936:G:A  0.250  -6.24e-8     0.250   4.08e- 8 FALSE  
#> 14 chr22:32122351:A:G -0.555  -5.68e-8    -0.556  -8.26e- 8 FALSE  
#> 15 chr22:32122676:A:G  0.718   8.85e-9     0.718  -1.66e- 8 FALSE  
#> 16 chr22:32123055:A:G -1.03   -2.65e-8    -1.03   -7.16e- 8 FALSE  
#> 17 chr22:32123164:T:C  0.834  -1.19e-7     0.834   2.60e- 7 FALSE  
#> 18 chr22:32123383:T:C -0.661  -7.59e-8    -0.662  -1.31e- 7 FALSE  
#> 19 chr22:32123461:T:C -0.0126  1.04e-8    -0.0126  3.42e-10 FALSE  
#> 20 chr22:32123806:C:T -0.430  -8.48e-8    -0.431  -9.55e- 8 FALSE  
#>