run_ora

[saezlab]

run_ora

[PauBadiaM]

Hi @elektrafying2000,

ora(docs) works by first sorting the genes of each cell based on their gene expression values and selecting an arbitrary amount of top expressed genes. By default it is the top 5%, meaning that if you have 100 genes in your mat you select only the top expressed 5 genes per cell, but this value can be set manually to be any number (n_up). The function also allows to select bottom genes (n_bottom) in cause you are working with gene contrast statistics obtained after DEG. In the end, you have a collection of genes per cell, that will be tested for over-representation using a one tailed fisher exact test against the gene sets stored in the database of your choice. ora also has a version that allows to run enrichment just by a list of genes with get_ora_df(docs), for when you don't have gene level statistics available to do the sorting.

Hope this is clear, please let me know if you have more questions.