how to use the p.adjust()-function

I got a list of p-values, obtained from two large datasets, by using the wilcox.test() function.

Since there's a multiple comparisons, I have to do adjustment of the p-values.

Problem is I just don't get how the p.adjust() function works.
Could someone please tell me step by step what to do, so I get adjusted p-values for all my known p-values?

Solution

I simply reproduce your data and bring this simple function:

dat <- data.frame(
    value=c(4409, 55.5, 3951.5),
    p.value=c(2.766e-15, 0.04606, 1.545e-15)
)

This is the simple function to get adjusted p-value:

getAdjustPval <- function(df, pAdjustMethod="BH", ...) {
    if(is.null(df$p.value)) {
        stop("p-value is required")
    } else {
        p <- df$p.value
        df$adjust.pvalue <- p.adjust(p, method = pAdjustMethod)
        df
    }
}

you'll get this:

   value   p.value adjust.pvalue
1 4409.0 2.766e-15     4.149e-15
2   55.5 4.606e-02     4.606e-02
3 3951.5 1.545e-15     4.149e-15