Within/intra group association in relevance network

Analysis
1

Hi all,

I wonder if there is a way to extract the edges between intra-group nodes in relevance network? For example, I have 2 omics data, one is based on amplicon sequencing of bacteria 16S rRNA and one is based on microeukaryotic 18S rRNA. I want to get not only bacteria-microeukaryotic associations but also bacteria-bacteria and microeukaryotic-microeukaryotic. Actually, in the real dataset, I have up to 4 groups, and I use diablo approach, so I want to extract 4 intra group associations as well.

2

hi @adyari808,

Unfortunately in our integrative approach, we are mostly interested in the inter associations.
One potential trick would be

  1. extract the name of the variables selected (selectVar()), then calculate the correlation within each omics (perhaps put a high threshold)
  2. extract the M matrix from your network result (sim.mat = network(nutri.res); sim.mat $M)
  3. combine those matrices (I dont know how) and input into cytoscape.

Or maybe cytoscape already has a function to calculate the correlations inter and intra based on step 1 above? Basically the idea is to use the mixOmics method you used as a filtering step for further downstream analysis.

Kim-Anh