Use Compass data with protein data

[BenjaminPLille]

Hi,
I use compass with mosaic from proteogenomic data. I would like to reuse the compass data (small sub-clones) with the phenotypic data to analyze the protein expression of the sub-clones. Is this possible?
Many thanks for your help
Benjamin

[e-sollier]

Hi,

COMPASS does not provide a direct analysis of subclone-specific expression data, but you should be able to do it indirectly.
COMPASS outputs a _cellAssignments.tsv file (see https://github.com/cbg-ethz/COMPASS?tab=readme-ov-file#output), which indicates to which node in the tree each cell was assigned. I have never worked with Tapestri protein data so I don't know how it looks like, but I suppose you should be able to use the cell assignments to look at subclones-specific protein expression.