findCellProximityGenes

Source: R/spatial_interaction.R

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