findCPG#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction.R#L1290

format

latex

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#

Argument

Description

...

Arguments passed on to `findICF <#findicf>`__ list(“?, ? “, list(list(list(?gobject?)), list(“giotto object?)), “?, ? “, list(list(list(?feat_type?)), list(“feature type?)), “?, ? “, list(list(list(?spat_unit?)), list(“spatial unit?)), “?, ? “, l ist(list(list(?expression_values?)), list(“expression values to use?)), “?, ? “, list(list(list(?selected_feats?)), list(“subset of selected features (optional)?)), “?, ? “, list(list(list(?cluster_column?)), list(“name of column to use for cell types?)), “?, ? “, 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("set_seed")), list("set a seed for reproducibility")), "\n", "    ", list(list(list("seed_number")), list("seed number")), "\n", "  ")

Seealso#

`findICF <#findicf>`__