findCPG: findCPG
In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description Usage Arguments Details Value Examples

Identifies genes that are differentially expressed due to proximity to other cell types.

findCPG(
  gobject,
  expression_values = "normalized",
  selected_genes = 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,
  cores = NA
)

`gobject`	giotto object
`expression_values`	expression values to use
`selected_genes`	subset of selected genes (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
`cores`	number of cores to use if do_parallel = TRUE

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 cpgObject contains - at least - the following columns:

genes: All or selected list of tested genes
sel: average gene expression in the interacting cells from the target cell type
other: average gene 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