kernel: Kernel Functions

In DISOhda/DiscreteFDR: FDR Based Multiple Testing Procedures with Adaptation for Discrete Tests

Kernel Functions

Description

Kernel functions that transform observed p-values or their support according to [HSU], [HSD], [AHSU], [AHSD] and [HBR-\lambda]. The output is used by discrete.BH or DBR, respectively. kernel_DBH_crit, kernel_ADBH_crit and kernel_DBR_crit additionally compute and return the critical constants. The end user should not use these functions directly.

Note: As of version 2.0, these functions are purely internal functions! As a consequence, they have to be called directly via :::, e.g. DiscreteFDR:::kernel_DBH_fast(). But users should not rely on them, as parameters (including their names, order, etc.) may be changed without notice!

Usage

kernel_DBH_fast(
  pCDFlist,
  pvalues,
  stepUp = FALSE,
  tau_max = NULL,
  alpha = 0.05,
  support = numeric(),
  pCDFcounts = NULL
)

kernel_DBH_crit(
  pCDFlist,
  support,
  sorted_pv,
  stepUp = FALSE,
  alpha = 0.05,
  pCDFcounts = NULL
)

kernel_ADBH_fast(
  pCDFlist,
  sorted_pv,
  stepUp = FALSE,
  alpha = 0.05,
  support = numeric(),
  pCDFcounts = NULL
)

kernel_ADBH_crit(
  pCDFlist,
  support,
  sorted_pv,
  stepUp = FALSE,
  alpha = 0.05,
  pCDFcounts = NULL
)

kernel_DBR_fast(pCDFlist, sorted_pv, lambda = 0.05, pCDFcounts = NULL)

kernel_DBR_crit(
  pCDFlist,
  support,
  sorted_pv,
  lambda = 0.05,
  alpha = 0.05,
  pCDFcounts = NULL
)

kernel_DBY_fast(pCDFlist, pvalues, pCDFcounts = NULL)

kernel_DBY_crit(pCDFlist, support, sorted_pv, alpha = 0.05, pCDFcounts = NULL)

Arguments

pCDFlist	list of the supports of the CDFs of the p-values; each list item must be a numeric vector, which is sorted in increasing order and whose last element equals 1.
pvalues	numeric vector, sorted in increasing order, that either must contain the entirety of all observable values of the p-value supports (when computing critical constants) or only the sorted raw p-values.
stepUp	boolean specifying whether to conduct the step-up (TRUE) or step-down (FALSE; the default) procedure.
tau_max	single real number strictly between 0 and 1 indicating the largest critical value for step-up procedures; if NULL (the default), it is computed automatically, otherwise it needs to be computed manually by the user; ignored if stepUp = FALSE.
alpha	single real number strictly between 0 and 1 indicating the target FDR level; for ⁠*_fast⁠ kernels, it is only needed, if stepUp = TRUE.
support	numeric vector, sorted in increasing order, that contains the entirety of all observable values of the p-value supports; for ⁠*_fast⁠ kernels, it is ignored if stepUp = FALSE.
pCDFcounts	integer vector of counts that indicates to how many p-values each unique p-value distributions belongs.
sorted_pv	numeric vector containing the raw p-values, sorted in increasing order.
lambda	real number strictly between 0 and 1 specifying the DBR tuning parameter.

Details

When computing critical constants under step-down, that is, when using kernel_DBH_crit, kernel_ADBH_crit or kernel_DBR_crit with stepUp = FALSE (i.e. the step-down case), we still need to get transformed p-values to compute the adjusted p-values.

Value

For kernel_DBH_fast(), kernel_ADBH_fast() and kernel_DBR_fast(), a vector of transformed p-values is returned. kernel_DBH_crit, kernel_ADBH_crit and kernel_DBR_crit return a list with critical constants (⁠$crit.consts⁠) and transformed p-values (⁠$pval.transf⁠), but if stepUp = FALSE, there are critical values only.

See Also

discrete.BH(), direct.discrete.BH(), DBR()

DISOhda/DiscreteFDR documentation built on April 14, 2025, 8:35 a.m.