Hi I’m trying to see if I can use the get.groups option to separate out my samples, I’ve checked out the get.groups wiki page and downloaded the folder for the examples. However, the wiki example of using get.groups with a shared file uses a “abrecovery.fn.shared” file which I can’t seem to find in the example folder I’ve downloaded. I’m not sure the layout of this shared file and how it would attach the OTUs to the sample ids as well as their grouping factors.
In my own work I’ve generated a shared file of my samples following subsampling and here is where I would like to separate out my groups of data.
I’ve run through the pipeline up to with my samples ids as 1, 2, 3, 4 ect.
My sample ids correspond to different grouping factors ie
1 – A
2 – B
3 – C
I can’t seem to figure out how to take the shared file that associates my samples with their OTUs (ie stability.opti_mcc.subsample.shared from the SOP) and then create a file that links up my sample OUTs from their ids with their grouping factor so I can then use the get.groups command and generate a new shared file that has removed the samples associated with the grouping factors I don’t want.