Confusion/doubts regarding community generation step in cna()

Hello Bio3d team,

I am using bio3d to compare the community structure of mutant and wildtype protein (from MD simulation)

and i am using following two commands to generate two networks.

netmax <- cna (cij, cm = cmapread, cuttof.cij=0.4,vnames=c(135:716),collapse.method="max") 
netmean <- cna (cij, cm = cmapread, cuttof.cij=0.5,vnames=c(135:716),collapse.method="mean")

Thereafter, i refine them using network amendment() to select community structure with slightly lower modularity score using following function (from tutorial section).

mod.select <- function(x, thres=0.1) {    
   remodel <- community.tree(x, rescale = TRUE)    
   n.max = length(unique(x$communities$membership))    
   ind.max = which(remodel$num.of.comms == n.max)    
   v = remodel$modularity[length(remodel$modularity):ind.max]    
   v = rev(diff(v))    
   fa = which(v>=thres)[1] - 1    
   ncomm = ifelse(is.na(fa), min(remodel$num.of.comms), n.max - fa)     
   ind <- which(remodel$num.of.comms == ncomm)    
   network.amendment(x, remodel$tree[ind, ])  
}

but output network for netmean and netmax are coming identical (irrespective of different cij cut-offs and different collapse methods).

Here are my queries regarding that,

1. The collapse.method variables (max, mean and median), uses maximum correlation value, or mean/median of correlation value of all pairs (which have edge between them) and their -log transformation as default edge between communities ?

2. Is network amendment script can be used in this very case ?

3. Identical output of different networks are generated because of call to cna() from network.amendment() uses only 'max' as default argument (which cant be changed by user, i think)? and hence different networks generated from different collapse methods are buffered by network amendment step ?

4. If i have to select community structure with lower modularity score overall, how should i make sure that correlation edges between those desired communities are result of max or mean collapse methods?

Thanks a lot!,

Comments (2)