findCellProximityGenes

Identifies cell-to-cell Interaction Changed Genes (ICG), i.e. genes that are differentially expressed due to proximity to other cell types.

findCellProximityGenes(...)

Arguments

...

...	Arguments passed on to `findInteractionChangedGenes` `gobject` giotto object `expression_values` expression values to use `selected_genes` subset of selected genes (optional) `cluster_column` name of column to use for cell types `spatial_network_name` name of spatial network to use `minimum_unique_cells` minimum number of target cells required `minimum_unique_int_cells` minimum number of interacting cells required `diff_test` which differential expression test `mean_method` method to use to calculate the mean `offset` offset value to use when calculating log2 ratio `adjust_method` which method to adjust p-values `nr_permutations` number of permutations if diff_test = permutation `exclude_selected_cells_from_test` exclude interacting cells other cells `do_parallel` run calculations in parallel with mclapply `cores` number of cores to use if do_parallel = TRUE `set_seed` set a seed for reproducibility `seed_number` seed number