You will use the find samples feature (highlighted below) to make subgroups:
First, search for all the samples you want in one of your subgroups. Next, click the Filter + Subgroup menu and choose 'New subgroup column'.
This will create a new column will be created with your subgroups. All the samples that matched your search term will be in one subgroup and all the samples that did not match your search term will in the other subgroup. The samples that matched your search term will be labeled as 'true' and those that did not will be labeled as 'false'.
In this example we are creating two subgroups: those that have EGFR aberrations (either mutations or copy number amplifications) and those that do not in TCGA Lung Adenocarcinoma.
Type '(mis OR infra) OR C:>0.5' into the samples search bar. This will select samples that either have a missense or inframe deletion '(mis OR infra)', or where copy number variation (column C) is greater than 0.5. Note that I arbitrarily choose a cutoff of 0.5.
Click the filter menu and select 'New column subgroup'. This will create a new column that has samples that met our search term marked as 'true' (ie. those that have an EGFR aberration) and those that did not meet our search term as 'false' (ie. those that do not have an EGFR aberration).