findCPG¶
findCPG
Description¶
- Identifies cell-to-cell Interaction Changed Genes (ICG),
i.e. genes that are differentially expressed due to proximity to other cell types.
Usage¶
findCPG(...)
Arguments¶
Argument |
Description |
|---|---|
|
Arguments passed on to ``findICG` <#findicg>`_ list(“n”, ” “, list(list(list(“gobject”)), list(“giotto object”)), “n”, ” “, list(list(list(“expression_values”)), list(“expression values to use”)), “n”, ” “, list(list(list(“selected_genes”)), list(“subset of selected genes (optional)”)), “n”, ” “, list(list(list(“cluster_column”)), list(“name of column to use for cell types”)), “n”, ” “, list(list(list(“spatial_network_name”)), list(“name of spatial network to use”)), “n”, ” “, list(list(list(“minimum_unique_cells”)), list( |
"minimum number of target cells required")), "\n", " ", list(list(list("minimum_unique_int_cells")), list("minimum number of interacting cells required")), "\n", " ", list(list(list("diff_test")), list("which differential expression test")), "\n", " ", list(list(list("mean_method")), list("method to use to calculate the mean")), "\n", " ", list(list(list("offset")), list("offset value to use when calculating log2 ratio")), "\n", " ", list(list(list("adjust_method")), list("which method to adjust p-values")),
"\n", " ", list(list(list("nr_permutations")), list("number of permutations if diff_test = permutation")), "\n", " ", list(list(list("exclude_selected_cells_from_test")), list("exclude interacting cells other cells")), "\n", " ", list(list(list("do_parallel")), list("run calculations in parallel with mclapply")), "\n", " ", list(list(list("cores")), list("number of cores to use if do_parallel = TRUE")), "\n", " ", list(list(list("set_seed")), list("set a seed for reproducibility")),
"\n", " ", list(list(list("seed_number")), list("seed number")), "\n", " ")
Seealso¶
``findICG` <#findicg>`_