Build mash Data-Driven Covariance Components

Build the raw per-method data-driven covariance components (cov_canonical / cov_pca / cov_flash / cov_flash(factors = "nonneg")) for a "strong" SumStats set – the reusable building block mashPriorCovariances then refines with an ED / udr engine. Exposed on its own so a workflow can build or inspect a single component (the mixture-prior notebook's per-method steps) without running the full prior.

Usage

mashCovarianceComponents(
  sumStatsList,
  alpha,
  vhat = NULL,
  components = c("canonical", "pca", "flash", "flash_nonneg"),
  nPcs = NULL,
  inputScale = c("auto", "beta", "z"),
  setSeed = 999
)

Arguments

sumStatsList: Named list (or S4Vectors::SimpleList) with at least "strong" (the discovery set the covariances are learned on).
alpha: mash alpha.
vhat: Residual correlation matrix (V); NULL -> identity.
components: Any of "canonical", "pca", "flash", "flash_nonneg". Built in that fixed order.
nPcs: PCs seeded into cov_pca. Default ncol(Bhat) - 1.
inputScale: SumStats -> matrix conversion scale.
setSeed: Integer seed (cov_flash is stochastic), or NULL to leave the ambient RNG untouched.

Value

A named list of covariance matrices (the concatenated components).

Examples

data(qtlSumStatsMulticontextExample)
ss <- qtlSumStatsMulticontextExample
sumStatsList <- list(strong = ss, random = ss)
mashCovarianceComponents(sumStatsList, alpha = 0)
#> Adding factor 1 to flash object...
#> Adding factor 2 to flash object...
#> Adding factor 3 to flash object...
#> Factor doesn't significantly increase objective and won't be added.
#> Wrapping up...
#> Done.
#> Backfitting 2 factors (tolerance: 8.94e-06)...
#>   Difference between iterations is within 1.0e+00...
#>   Difference between iterations is within 1.0e-01...
#>   Difference between iterations is within 1.0e-02...
#>   Difference between iterations is within 1.0e-03...
#>   Difference between iterations is within 1.0e-04...
#> Wrapping up...
#> Done.
#> Adding factor 1 to flash object...
#> Adding factor 2 to flash object...
#> Adding factor 3 to flash object...
#> Factor doesn't significantly increase objective and won't be added.
#> Wrapping up...
#> Done.
#> Backfitting 2 factors (tolerance: 8.94e-06)...
#>   Difference between iterations is within 1.0e+00...
#>   Difference between iterations is within 1.0e-01...
#>   Difference between iterations is within 1.0e-02...
#>   Difference between iterations is within 1.0e-03...
#> Wrapping up...
#> Done.
#> $identity
#>      [,1] [,2] [,3]
#> [1,]    1    0    0
#> [2,]    0    1    0
#> [3,]    0    0    1
#> 
#> $brain
#>      [,1] [,2] [,3]
#> [1,]    1    0    0
#> [2,]    0    0    0
#> [3,]    0    0    0
#> 
#> $blood
#>      [,1] [,2] [,3]
#> [1,]    0    0    0
#> [2,]    0    1    0
#> [3,]    0    0    0
#> 
#> $muscle
#>      [,1] [,2] [,3]
#> [1,]    0    0    0
#> [2,]    0    0    0
#> [3,]    0    0    1
#> 
#> $equal_effects
#>      [,1] [,2] [,3]
#> [1,]    1    1    1
#> [2,]    1    1    1
#> [3,]    1    1    1
#> 
#> $simple_het_1
#>      [,1] [,2] [,3]
#> [1,] 1.00 0.25 0.25
#> [2,] 0.25 1.00 0.25
#> [3,] 0.25 0.25 1.00
#> 
#> $simple_het_2
#>      [,1] [,2] [,3]
#> [1,]  1.0  0.5  0.5
#> [2,]  0.5  1.0  0.5
#> [3,]  0.5  0.5  1.0
#> 
#> $simple_het_3
#>      [,1] [,2] [,3]
#> [1,] 1.00 0.75 0.75
#> [2,] 0.75 1.00 0.75
#> [3,] 0.75 0.75 1.00
#> 
#> $PCA_1
#>            brain     blood    muscle
#> brain  0.2031844 0.3340120 0.2243579
#> blood  0.3340120 0.5490777 0.3688188
#> muscle 0.2243579 0.3688188 0.2477379
#> 
#> $PCA_2
#>               brain       blood      muscle
#> brain   0.003729395  0.03240844 -0.05162538
#> blood   0.032408439  0.28162928 -0.44862448
#> muscle -0.051625382 -0.44862448  0.71464133
#> 
#> $tPCA
#>             brain      blood     muscle
#> brain  0.03035490 0.05053652 0.03216785
#> blood  0.05053652 0.08860772 0.04406890
#> muscle 0.03216785 0.04406890 0.05421172
#> 
#> $tFLASH_default
#>             brain      blood     muscle
#> brain  0.02925699 0.04153723 0.02668673
#> blood  0.04153723 0.05976538 0.04117086
#> muscle 0.02668673 0.04117086 0.03792385
#> 
#> $FLASH_default_1
#>            brain     blood    muscle
#> brain  0.2369678 0.3444523 0.2493325
#> blood  0.3444523 0.5006899 0.3624253
#> muscle 0.2493325 0.3624253 0.2623423
#> 
#> $FLASH_default_2
#>             brain      blood     muscle
#> brain   0.2390964  0.1950579 -0.3793174
#> blood   0.1950579  0.1591308 -0.3094521
#> muscle -0.3793174 -0.3094521  0.6017728
#> 
#> $tFLASH_nonneg
#>             brain      blood     muscle
#> brain  0.02858018 0.04225972 0.02669381
#> blood  0.04225972 0.06248734 0.03955125
#> muscle 0.02669381 0.03955125 0.03703607
#> 
#> $FLASH_nonneg_1
#>            brain     blood    muscle
#> brain  0.2370147 0.3505876 0.2406804
#> blood  0.3505876 0.5185825 0.3560099
#> muscle 0.2406804 0.3560099 0.2444028
#> 
#> $FLASH_nonneg_2
#>               brain        blood       muscle
#> brain  8.739128e-07 7.525978e-06 0.0009348023
#> blood  7.525978e-06 6.481236e-05 0.0080503477
#> muscle 9.348023e-04 8.050348e-03 0.9999343137
#>

Usage

Arguments

Value

See also

Examples