findICF#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction.R#L1220

Description#

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

Usage#

findICF(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = "normalized",
  selected_feats = NULL,
  cluster_column,
  spatial_network_name = "Delaunay_network",
  minimum_unique_cells = 1,
  minimum_unique_int_cells = 1,
  diff_test = c("permutation", "limma", "t.test", "wilcox"),
  mean_method = c("arithmic", "geometric"),
  offset = 0.1,
  adjust_method = c("bonferroni", "BH", "holm", "hochberg", "hommel", "BY", "fdr",
    "none"),
  nr_permutations = 100,
  exclude_selected_cells_from_test = T,
  do_parallel = TRUE,
  set_seed = TRUE,
  seed_number = 1234
)

Arguments#

Argument

Description

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

exclu de_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

Details#

Function to calculate if genes are differentially expressed in cell types when they interact (approximated by physical proximity) with other cell types. The results data.table in the icfObject contains - at least - the following columns:

  • features: All or selected list of tested features

  • sel: average feature expression in the interacting cells from the target cell type

  • other: average feature expression in the NOT-interacting cells from the target cell type

  • log2fc: log2 fold-change between sel and other

  • diff: spatial expression difference between sel and other

  • p.value: associated p-value

  • p.adj: adjusted p-value

  • cell_type: target cell type

  • int_cell_type: interacting cell type

  • nr_select: number of cells for selected target cell type

  • int_nr_select: number of cells for interacting cell type

  • nr_other: number of other cells of selected target cell type

  • int_nr_other: number of other cells for interacting cell type

  • unif_int: cell-cell interaction

Value#

icfObject that contains the Interaction Changed differential gene scores

Seealso#

`findInteractionChangedFeats <#findinteractionchangedfeats>`__