kernel {DiscreteFDR}R Documentation

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. Additionally, kernel.DBH.crit, kernel.ADBH.crit and kernel.DBR.crit compute and return the critical constants. The end user should not use these functions directly.

Usage

kernel_DBH_fast(pCDFlist, pvalues, stepUp = FALSE, alpha = 0.05, support = 0L)

kernel_DBH_crit(pCDFlist, pvalues, sorted_pv, stepUp = FALSE, alpha = 0.05)

kernel_ADBH_fast(pCDFlist, pvalues, stepUp = FALSE, alpha = 0.05, support = 0L)

kernel_ADBH_crit(pCDFlist, pvalues, sorted_pv, stepUp = FALSE, alpha = 0.05)

kernel_DBR_fast(pCDFlist, pvalues, lambda = 0.05)

kernel_DBR_crit(pCDFlist, pvalues, sorted_pv, lambda = 0.05, alpha = 0.05)

Arguments

pCDFlist

a list of the supports of the CDFs of the p-values. Each support is represented by a vector that must be in increasing order.

pvalues

a numeric vector. Contains all values of the p-values supports if we search for the critical constants. If not, contains only the observed p-values. Must be sorted in increasing order!

stepUp

a numeric vector. Identical to pvalues for a step-down procedure. Equals c.m for a step-up procedure.

alpha

the target FDR level, a number strictly between 0 and 1. For *.fast kernels, it is only necessary, if stepUp = TRUE.

support

a numeric vector. Contains all values of the p-values supports. Ignored, if stepUp = FALSE. Must be sorted in increasing order!

sorted_pv

a vector of observed p-values, in increasing order.

lambda

a number strictly between 0 and 1. If lambda=NULL (by default), then lambda is chosen equal to alpha.

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.

This version: 2019-11-15.

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 object with critical constants ($crit.consts) and transformed p-values ($pval.transf), but if stepUp = FALSE, there are critical values only.

See Also

discrete.BH, DiscreteFDR, DBR

Examples

X1 <- c(4, 2, 2, 14, 6, 9, 4, 0, 1)
X2 <- c(0, 0, 1, 3, 2, 1, 2, 2, 2)
N1 <- rep(148, 9)
N2 <- rep(132, 9)
Y1 <- N1 - X1
Y2 <- N2 - X2
df <- data.frame(X1, Y1, X2, Y2)
df

#Construction of the p-values and their support
df.formatted <- fisher.pvalues.support(counts = df, input = "noassoc")
raw.pvalues <- df.formatted$raw
pCDFlist <- df.formatted$support

alpha <- 0.05

# Compute the step functions from the supports

# We stay in a step-down context, where pv.numer = pv.denom,
# for the sake of simplicity

# If not searching for critical constants, we use only the observed p-values
sorted.pvals <- sort(raw.pvalues)
y.DBH.fast <- kernel_DBH_fast(pCDFlist, sorted.pvals)
y.ADBH.fast <- kernel_ADBH_fast(pCDFlist, sorted.pvals)
# transformed values
y.DBH.fast
y.ADBH.fast

# compute transformed support
pv.list <- sort(unique(unlist(pCDFlist)))
y.DBH.crit <- kernel_DBH_crit(pCDFlist, pv.list, sorted.pvals)
y.ADBH.crit <- kernel_ADBH_crit(pCDFlist, pv.list, sorted.pvals)
y.DBR.crit <- kernel_DBR_crit(pCDFlist, pv.list, sorted.pvals)
# critical constants
y.DBH.crit$crit.consts
y.ADBH.crit$crit.consts
y.DBR.crit$crit.consts
# The following exist only for step-down direction or DBR
y.DBH.crit$pval.transf
y.ADBH.crit$pval.transf
y.DBR.crit$pval.transf


[Package DiscreteFDR version 1.3.6 Index]