Running GSEA for for mouse Liana x tensor-cell2cell

[wgao688]

I am trying to run this code for a mouse dataset (https://ccc-protocols.readthedocs.io/en/latest/notebooks/ccc_R/QuickStart.html):

# Generate list with ligand-receptors pairs in DB
lr_pairs <- liana::select_resource('Consensus')[[1]] %>%
    select(ligand = source_genesymbol, receptor = target_genesymbol)
lr_list <- lr_pairs %>%
     unite('interaction', ligand, receptor, sep = '^') %>%
     pull(interaction)

# Specify the organism and pathway database to use for building the LR set
organism = "human"
pathwaydb = "KEGG"

# Generate ligand-receptor gene sets
lr_set <- c2c$external$generate_lr_geneset(lr_list = lr_list,
                                           complex_sep='_', # Separation symbol of the genes in the protein complex
                                           lr_sep='^', # Separation symbol between a ligand and a receptor complex
                                           organism=organism,
                                           pathwaydb=pathwaydb,
                                           readable_name=TRUE
                                           )

Change the organism = "mouse" does not work. I have been able to run the Liana x tensor-cell2cell up to this point. Thanks!

[earmingol]

Hi! using mouse doesn't support pathwaydb="KEGG", you have to change it to pathwaydb="GOBP" or pathwaydb="Reactome"