Question: WGCNA: outputting multiple hubgenes from a module
0
gravatar for RNAseqer
5 weeks ago by
RNAseqer 130
RNAseqer 130 wrote:

I know that WGCNA has the function chooseTopHubInEachModule() to pick the gene with the single highest connectivity within a module, but does it have a function to output several hubgenes from a module? Im looking through the manual and it certainly seems like it should be a straightforward task but I'm having some trouble executing it, so I thought I'd just ask if anyone had done this before.

wgcna hubgenes • 95 views
ADD COMMENTlink modified 5 weeks ago by Kevin Blighe61k • written 5 weeks ago by RNAseqer 130
1
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

Hi,

I would honestly just hack the function code and create my own function, if I were you. The code is simple:

WGCNA::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 line that you'll probably want to change is:

hub = which.max(rowSums(adj))

Note that there are many hub-selection metrics.

Kevin

ADD COMMENTlink written 5 weeks ago by Kevin Blighe61k
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