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ksavell / XPoSE

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Inclusion threshold for pseudobulk #36

Closed ksavell closed 4 months ago

ksavell commented 1 year ago

In figure2.R line 66, I expect all clusters to be ran for glut since there are > 100 nuclei per cluster in each cluster. 

         CTL6 CTL6b ITL23 ITL56 NPL56 PTL5

Active 334 6 525 737 26 233 Homecage 2817 295 2824 2913 464 1271 Non-active 1121 100 1306 1262 180 598

Table: Non-active Homecage ITL56 737 2913 ITL23 525 2824 CTL6 334 2817 PTL5 233 1271

However, I think it's still using Active for the inclusion criteria despite what is in the comp_vect spot

ksavell commented 1 year ago

As a quick fix I omitted lines 21 to 46 in run_pseudobulk.R and replaced with incl_clust <- unique(object$cluster_name) to pull all clusters