Group_permute edges between networks

[Femke Lammertink]

Dear Chris,

I was wondering whether it is possible to (statistically) test the difference between network edges, using the permute function. More specifcally, using the  count_inter function I would be able to sum the edges between and within networks (DMN, SN, ECN). I tried to adapt the function (see below) so it incorperates the new measure, but I'm doing something wrong as it gives the following error:   task 1 failed - "error in evaluating the argument 'x' in selecting a method for function 't': inherits(g, "brainGraph") is not TRUE"

strength.diffs.perm <- function(g, densities) {

  meas <- lapply(g, function(x) t(sapply(x, function(y) count_inter(y)$mat[1,1])))

  meas.diff <- sapply(seq_along(V(g[[1]][[1]])), function(x)

    brainGraph:::auc_diff(densities, cbind(meas[[1]][, x], meas[[2]][, x])))

  tmp <- as.data.table(t(meas.diff))

  setnames(tmp, 1:ncol(tmp), V(g[[1]][[1]])$name)

  return(tmp)

}

 

Would it be possible to resolve this issue? Of maybe there's a different approach (e.g. using the "degree" function)? Ideally, I'd like to test the difference between groups (time 1/time 2) within each network, but also test the differences between network edges within one timepoint.

Many thanks in advance.

Best wishes, Femke

[Chris Watson]

I'm not sure what you mean by "test the differences between network edges", but it looks like you are interested in the between-group difference of subgraph sizes/densities (where your subgraphs are the DMN, SN, etc.). Your code looks correct so I am not sure what the error is.

You can first try passing a nested list of graph objects to your custom function and see if that runs without error.

Chris

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[Femke Lammertink]

Dear Chris,

My apologies for not being clear. I'd indeed like to compare the number of connections (at different density levels) between networks. 

How should I construct a nested list of graph objects? Do you have some pointers? 

Femke

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[Chris Watson]

Please see the User Guide, Chapter 6.

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