pVal2lfdr: Convert p-values to lfdr

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

Convert p-values to lfdr

Description

This function takes a numeric vector of p-values and returns a vector of lfdr-values (local false discovery) using the package fdrtool. Multiple testing correction should be performed with caution, short series of p-values typically pose problems for transforming to lfdr. The transformation to lfdr values may give warning messages, in this case the resultant lfdr values may be invalid !

Usage

pVal2lfdr(x, silent = TRUE, debug = FALSE, callFrom = NULL)

Arguments

x	(numeric) vector of p.values
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allow easier tracking of messages produced

Value

This function returns a (numeric) vector of lfdr values (or NULL if data insufficient to run the function 'fdrtool')

See Also

lfdr from fdrtool, other p-adjustments (multiple test correction, eg FDR) in p.adjust

Examples

## Note that this example is too small for estimating really meaningful fdr values
## In consequence, a warning will be issued.
set.seed(2017); t8 <- matrix(round(rnorm(160,10,0.4),2), ncol=8,
  dimnames=list(letters[1:20], c("AA1","BB1","CC1","DD1","AA2","BB2","CC2","DD2")))
t8[3:6,1:2] <- t8[3:6,1:2]+3   # augment lines 3:6 (c-f) for AA1&BB1
t8[5:8,5:6] <- t8[5:8,5:6]+3   # augment lines 5:8 (e-h) for AA2&BB2 (c,d,g,h should be found)
head(pVal2lfdr(apply(t8, 1, function(x) t.test(x[1:4], x[5:8])$p.value)))

wrMisc documentation built on Sept. 11, 2024, 6:10 p.m.