exprCellCellcom: exprCellCellcom

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

exprCellCellcom

Description

Cell-Cell communication scores based on expression only

Usage

exprCellCellcom(
  gobject,
  cluster_column = "cell_types",
  random_iter = 1000,
  gene_set_1,
  gene_set_2,
  log2FC_addendum = 0.1,
  detailed = FALSE,
  adjust_method = c("fdr", "bonferroni", "BH", "holm", "hochberg", "hommel", "BY",
    "none"),
  adjust_target = c("genes", "cells"),
  set_seed = TRUE,
  seed_number = 1234,
  verbose = T
)

Arguments

gobject	giotto object to use
cluster_column	cluster column with cell type information
random_iter	number of iterations
gene_set_1	first specific gene set from gene pairs
gene_set_2	second specific gene set from gene pairs
log2FC_addendum	addendum to add when calculating log2FC
detailed	provide more detailed information (random variance and z-score)
adjust_method	which method to adjust p-values
adjust_target	adjust multiple hypotheses at the cell or gene level
set_seed	set seed for random simulations (default = TRUE)
seed_number	seed number
verbose	verbose

Details

Statistical framework to identify if pairs of genes (such as ligand-receptor combinations) are expressed at higher levels than expected based on a reshuffled null distribution of gene expression values, without considering the spatial position of cells. More details will follow soon.

Value

Cell-Cell communication scores for gene pairs based on expression only

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.