Arguments For The DENTIST LD-Mismatch Check

Options for dentistSingleWindow, pecotmr's DENTIST implementation. Every field is a formal of that function, so an unknown name is rejected by R as an unused argument; there is no ... because the contract is complete. Pass the result as ldMismatchQc(method = ) or summaryStatsQc(ldMismatchQcMethod = ).

Usage

DentistParam(
  pValueThreshold = 5e-08,
  propSVD = 0.4,
  gcControl = FALSE,
  nIter = 10,
  gPvalueThreshold = 0.05,
  duprThreshold = 0.99,
  numThreads = 1,
  correctChenEtAlBug = TRUE,
  seed = NULL
)

Arguments

pValueThreshold

Significance threshold for the DENTIST statistic. Default 5e-8.

propSVD

Proportion of the singular value decomposition retained. Default 0.4.

gcControl

Logical; apply genomic control. Default FALSE.

nIter

Number of DENTIST iterations. Default 10.

gPvalueThreshold

Grouping p-value threshold. Default 0.05.

duprThreshold

Duplicate r-squared threshold. Default 0.99.

numThreads

Number of CPU cores. Default 1.

correctChenEtAlBug

Logical; apply the Chen et al. correction. Default TRUE.

seed

Integer or NULL. Random seed for the iteration.

Value

A DentistParam object, a MethodParam.

Examples

DentistParam(propSVD = 0.5)
#> <DentistParam>
#>   pValueThreshold          5e-08
#>   propSVD                  0.5
#>   gcControl                FALSE
#>   nIter                    10
#>   gPvalueThreshold         0.05
#>   duprThreshold            0.99
#>   numThreads               1
#>   correctChenEtAlBug       TRUE
#>   unset: seed