Save cell expression - cell expression association patterns for simulation

Usage

ExprExprTable(
  gobject,
  database = c("mouse", "human", "external"),
  external_database_path = NULL,
  region_specific = F,
  spatial_network_name,
  p_adj = 0.05,
  abs_log2fc_LR = 0.25,
  output_file = file.path(getwd(), "est_CCI_expr_expr.csv"),
  seed = NULL
)

Arguments

gobject: Giotto object, output of preprocessGiotto.
database: Specify databases for pairs of genes for consideration. Possible values include "mouse", "human", and "external". The "mouse" and "human" are ligand-receptor pairs downloaded from CellTalkDB. If "external" is used, users also need to provide value for external_database_path.
external_database_path: A path and file name to external gene-gene pair database.
region_specific: Perform the analysis separately for each region.
spatial_network_name: Networks to choose. Possible values include "Delaunay_network", "distance_based_network", "knn_network".
p_adj: Adjusted p-value threshold (Default = 0.05) for saving.
abs_log2fc_LR: Effect size threshold for saving.
output_file: Provide a path and file name to save the CCI results for use in sCCIgen.
seed: Seed.