call_cellchat: Run CellChat with OmniPath function [[DEPRECATED]]

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Run CellChat with OmniPath function [[DEPRECATED]]

Description

Run CellChat with OmniPath function [[DEPRECATED]]

Usage

call_cellchat(
  sce,
  op_resource,
  .format = TRUE,
  exclude_anns = c(),
  nboot = 100,
  assay = "RNA",
  .seed = 1004,
  .normalize = FALSE,
  .do_parallel = FALSE,
  .raw_use = TRUE,
  expr_prop = 0,
  organism = "human",
  thresh = 1,
  de_thresh = 0.05,
  ...
)

Arguments

sce	Seurat object as input
op_resource	OmniPath Intercell Resource DN
.format	bool whether to format output
exclude_anns	Annotation criteria to be excluded
nboot	number of bootstraps to calculate p-value
assay	assay name (RNA by default)
.seed	random seed
.normalize	# bool whether to normalize non-normalized data with
.do_parallel	whether to parallelize or not
.raw_use	whether use the raw data or gene expression data projectected to a ppi (should be kept to TRUE)
expr_prop	minimum proportion of gene expression per cell type (0 by default), yet perhaps one should consider setting this to an appropriate value between 0 and 1, as an assumptions of these method is that communication is coordinated at the cluster level.
organism	Obtain CellChatDB for which organism ('mouse' or 'human')
thresh	p-value threshold (1 by default)
de_thresh	diff expression of genes p-value
...	Arguments passed on to CellChat::subsetCommunication object CellChat object net Alternative input is a data frame with at least with three columns defining the cell-cell communication network ("source","target","interaction_name") slot.name the slot name of object: slot.name = "net" when extracting the inferred communications at the level of ligands/receptors; slot.name = "netP" when extracting the inferred communications at the level of signaling pathways sources.use a vector giving the index or the name of source cell groups targets.use a vector giving the index or the name of target cell groups. signaling a character vector giving the name of signaling pathways of interest pairLR.use a data frame consisting of one column named either "interaction_name" or "pathway_name", defining the interactions of interest datasets select the inferred cell-cell communications from a particular 'datasets' when inputing a data frame 'net' ligand.pvalues,ligand.logFC,ligand.pct.1,ligand.pct.2 set threshold for ligand genes ligand.pvalues: threshold for pvalues in the differential expression gene analysis (DEG) ligand.logFC: threshold for logFoldChange in the DEG analysis; When ligand.logFC > 0, keep upgulated genes; otherwise, kepp downregulated genes ligand.pct.1: threshold for the percent of expressed genes in the defined 'positive' cell group. keep genes with percent greater than ligand.pct.1 ligand.pct.2: threshold for the percent of expressed genes in the cells except for the defined 'positive' cell group receptor.pvalues,receptor.logFC,receptor.pct.1,receptor.pct.2 set threshold for receptor genes

Details

CellChat's objects are not lazily documented/exported thus the whole package has to be imported.

Value

A DF of intercellular communication network

saezlab/liana documentation built on Aug. 10, 2024, 8:14 a.m.