### Name: p.adjust
### Title: Adjust P-values for Multiple Comparisons
### Aliases: p.adjust p.adjust.methods
### Keywords: htest

### ** Examples

require(graphics)

set.seed(123)
x <- rnorm(50, mean=c(rep(0,25),rep(3,25)))
p <- 2*pnorm( sort(-abs(x)))

round(p, 3)
round(p.adjust(p), 3)
round(p.adjust(p,"BH"), 3)

## or all of them at once (dropping the "fdr" alias):
p.adjust.M <- p.adjust.methods[p.adjust.methods != "fdr"]
p.adj <- sapply(p.adjust.M, function(meth) p.adjust(p, meth))
round(p.adj, 3)
## or a bit nicer:
noquote(apply(p.adj, 2, format.pval, digits = 3))

## and a graphic:
matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp=1, lty=1:6,
        main = "P-value adjustments")
legend(.7,.6, p.adjust.M, col=1:6, lty=1:6)

## Can work with NA's:
pN <- p; iN <- c(46,47); pN[iN] <- NA
pN.a <- sapply(p.adjust.M, function(meth) p.adjust(pN, meth))
## The smallest 20 P-values all affected by the NA's :
round((pN.a / p.adj)[1:20, ] , 4)