I have a matrix of p-values (named Fisher) and I calculated adjusted p-values using multtest like this:

> class(Fisher)
[1] "matrix"
AdjPvalues = mt.rawp2adjp(Fisher, proc=c("Bonferroni"))
> class(AdjPvalues)
[1] "list"

The output is a list, but I am not sure how to access (understand) it. I want to extract gene pairs with an adjusted p-value < 0.05. But how can I remake a matrix with gene pairs and their p-values?

Here's some info about AdjPvalues:

> head(AdjPvalues$adjp)
rawp Bonferroni
[1,]    0          0
[2,]    0          0
[3,]    0          0
[4,]    0          0
[5,]    0          0
[6,]    0          0

> head(AdjPvalues$index)
[1]     1  2688  5375  8062 10749 13436
> head(AdjPvalues$h0.ABH)
NULL
> head(AdjPvalues$h0.TSBH)
NULL

The matrix Fisher contained names of the gene pairs, and I would like to output the gene pairs and the adjusted p-values from AdjPvalues

A few lines from Fisher:

row.names   scigt000002 scigt000019 scigt000020
1   scigt000002 0.000000e+00    2.195239e-01    8.305768e-01
2   scigt000019 2.195239e-01    0.000000e+00    1.059412e-0
3   scigt000020 8.305768e-01    1.059412e-02    0.000000e+00

No need for the multest package, just code in plain R:

gene <- colnames(Fisher)
gene.pair <- paste(gene[row(Fisher)], gene[col(Fisher)], sep=".")
i <- lower.tri(Fisher)
Dat <- data.frame(gene.pair[i], p.value=Fisher[i])
Dat$Holm <- p.adjust(Dat$p.value, method="holm")
Dat