search

songw01 / MEGENA

Multiscale embedded gene co-expression network analysis
GNU General Public License v3.0
48 stars 16 forks source link

Multiscale organization of functions/pathways #6

Open nfancy opened 3 years ago

nfancy commented 3 years ago

Hi,

Thanks for the package. I am a new user of the package and trying to get the meaning of the output. In your paper, figure-9, there is a description of multi scale clusters. In the descrtion it is mentioned that " Fig 9A shows that the combination of all the clusters across the different scale groups consistently outperforms the individual scale groups across almost the entire range of significance levels." however, in the MEGENA.output I can see there are tables for different scales in here : MEGENA.output$hub.output$hub.stat s1-s4 for example.

My question is the final clustering that we get in the summary.output is that based on all the clusters across the different scale?

Also what does the module.scale column in the summary.output$module.table mean? Some of the rows are NA in this column, does it mean that is the all scale? I am actually a bit confused on the whole scale thing.

My request is, is it possible to add some explanation on the different output that we get after the analysis in the vignette?

Many thanks.

Nurun

songw01 commented 3 years ago

Hi, Nurun,

While the resolution parameter alpha is a continuous value to define clusters at different scales, the S1-S4 represent discretized alpha values to group the modules with close alpha values. To that end, it may be marginally useful to navigate modules at discretized resolutions, but I rather recommend to use all significant modules with module p-value < 0.05.

Regards,