Arguments For RAISS Imputation During Summary-Statistic QC

The settings summaryStatsQc uses when impute = TRUE. Five are forwarded to raiss; the other four are pecotmr's own, bounding which panel variants RAISS is asked to impute and how wide a window it reads.

rcond applies whatever the collection's LD reference is: QC hands RAISS a genotype panel's dosages, which route through the SVD solver, or an LdMatrix's correlations, which are inverted directly, and both drop the same weak directions. svdTol only matters on the genotype route.

Usage

RaissParam(
  lamb = 0.01,
  rcond = 0.01,
  svdTol = 1e-12,
  r2Threshold = 0.6,
  minimumLd = 5,
  mafCutoff = 0,
  macCutoff = 0,
  imissCutoff = 1,
  flank = 0
)

Arguments

lamb

Regularization term added to the LD diagonal. Default 0.01.

rcond

Eigenvalue cutoff for the pseudo-inverse of the known variants' LD: directions whose ridged eigenvalue is below rcond times the largest are dropped. Default 0.01, as raiss's own.

svdTol

Relative tolerance below which singular values of the standardized genotypes are treated as numerically zero, used when the LD reference is a genotype panel. Default 1e-12. Note this is tighter than raiss's own 1e-8 default.

r2Threshold

Imputation \(R^2\) below which a variant is dropped from the output. Default 0.6.

minimumLd

Minimum LD score for retaining an imputed variant. Default 5.

mafCutoff

Minor-allele-frequency floor for a variant to be an imputation TARGET. Default 0.

macCutoff

Minor-allele-count floor for a target; the stricter of this and mafCutoff applies. Default 0.

imissCutoff

Missingness ceiling for a target. Default 1.

flank

Base pairs by which to widen the analysis-region window on each side, retaining LD context for edge variants. Default 0.

Value

A RaissParam object, a MethodParam.

See also

summaryStatsQc, raiss

Examples

RaissParam(mafCutoff = 0.01, flank = 5e5)
#> <RaissParam>
#>   lamb                     0.01
#>   rcond                    0.01
#>   svdTol                   1e-12
#>   r2Threshold              0.6
#>   minimumLd                5
#>   mafCutoff                0.01
#>   macCutoff                0
#>   imissCutoff              1
#>   flank                    5e+05