The part of the function that handles p.value is:

    if (p.value < 1) {
        sig <- adj.p.val[o] <= p.value
        sig[is.na(sig)] <- FALSE
        tab <- tab[sig, ]
    }

I think it works as intended if it is adjusted to:

    if (p.value < 1) {

        sig <- tab$PValue <= p.value
        
        sig[is.na(sig)] <- FALSE
        tab <- tab[sig, ]
    }

Dear Alexander,

Thanks for taking the time to make a post, but have you read the document for the topTags function to fully understand what it is intended to do? In order to identify or report a bug, you need to identify an example in which the function doesn't do what it is supposed to do, according to the documentation. You need to actually run the function to show that it gives the wrong answer. Just saying you think that the code should be different without giving a reason isn't the way it works.

Best wishes
Gordon