This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Hub selection in WGCNA

In WGCNA package, there is a function chooseTopHubInEachModule that selects top hub genes from each module of the network. Which filters and cut-off does it use for hub selection?

Thanks

wgcna hubs
• 8,336 views • link
updated by Kevin Blighe Kevin Blighe • written by grant.hovhannisyan grant.hovhannisyan

1 answer

There are different ways to calculate hub scores. WGCNA's implementation is to simply return the gene with the maximum adjacency / 'connectivity' per module. Just type chooseTopHubInEachModule on your command line:

chooseTopHubInEachModule
function (datExpr, colorh, omitColors = "grey", power = 2, type = "signed", 
    ...) 
{
    isIndex = FALSE
    modules = names(table(colorh))
    if (!is.na(omitColors)[1])) 
        modules = modules[!is.element(modules, omitColors)]
    if (is.null(colnames(datExpr))) {
        colnames(datExpr) = 1:dim(datExpr)[2]
        isIndex = TRUE
    }
    hubs = rep(NA, length(modules))
    names(hubs) = modules
    for (m in modules) {
        adj = adjacency(datExpr[, colorh == m], power = power, 
            type = type, ...)
        hub = which.max(rowSums(adj))
        hubs[m] = colnames(adj)[hub]
    }
    if (isIndex) {
        hubs = as.numeric(hubs)
        names(hubs) = modules
    }
    return(hubs)
}

The key lines are within the for loop.

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

Thanks, very helpful! So as far as I understand, chooseTopHubInEachModule selects only one hub per module? I got confused because of the name of the function, thinking that one hub per module is calculated by chooseOneHubInEachModule.

• 0 views • link
written by grant.hovhannisyan grant.hovhannisyan

I do not know what the utility is of the chooseOneHubInEachModule function. However, regarding the WGCNA package, there appears to be redundancy (in terms of code) across its various functions. Important to remember that WGCNA is not a Bioconductor package.

• 0 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this