deprecated — findCellProximityGenes • Giotto

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

findCellProximityGenes(...)

Arguments

...

Arguments passed on to findInteractionChangedFeats

gobject: giotto object
feat_type: feature type
spat_unit: spatial unit
expression_values: expression values to use
selected_feats: subset of selected features (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
set_seed: set a seed for reproducibility
seed_number: seed number

Value

cell-cell interaction changed genes

See also

findInteractionChangedFeats