findCPG

Last Updated: Jan 29, 2024

Description

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

Usage

findCPG(...)

Arguments

...

Arguments passed on to findICF 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_tes t : exclude interacting cells other cells do_parallel run calculations in parallel with mclapply set_seed set a seed for reproducibility seed_number seed number

See Also

findICF