GenerateEdgeWeights: Generates files of cluster:ligand:receptor:cluster edge...

In VCCRI/scTalk: Single-cell talk - an R package for analysis of cell-cell communication networks from single-cell data.

Description

For a Seurat object, calculates all edge weights connecting source cell populations to ligands, ligands to receptors and receptors to target cell populations. Cell-ligand and receptor-cell edge weights are defined as the log2 fold-change difference in expression of the gene in that cell type relative to all other cell types in the Seurat object - as defined by the active identities. The ligand:receptor edge weights are assigned using protein:protein association scores from the STRING database.

Usage

GenerateEdgeWeights(
  seurat.object,
  file.label,
  species,
  populations.use = NULL,
  pct.threshold = 0.1,
  use.string.offline = TRUE,
  string.dir = NULL,
  string.ver = NULL,
  string.receptors = NULL,
  string.ligands = NULL,
  string.input.map = NULL,
  string.evidence.class = "combined_score",
  verbose = FALSE
)

Arguments

seurat.object	a list of genes
file.label	a Seurat object with cluster identities
species	species of the experiment - currently includes 'human' and 'mouse'
populations.use	threshold of percentage of cells expressing the gene in a cluster for it to be considered expressed
pct.threshold	percentage of cells in a cluster expressing a gene for it to be considered
use.string.offline	whether to use packaged STRING scores (default) or retrieve online from STRINGdb
string.dir	directory for storing retrieved online STRING data (defaults to working directory)
string.ver	version of online STRING data-base to use. Not set by default.
string.receptors	a list of receptor names that STRING recognises (if cannot map defaults)
string.ligands	a list of ligand names that STRING recegnises (if cannot map defaults)
string.input.map	named vector of STRING-compatable gene symbols with names corresponding to genes in dataset
string.evidence.class	what STRING evidence class to use. Defaults to 'combined_score'. Alternatives are: "neighborhood", "neighborhood_transferred", "fusion", "cooccurence", "homology", "coexpression", "coexpression_transferred", "experiments", "experiments_transferred", "database", "database_transferred", "textmining" and "textmining_transferred"
verbose	whether to print additional information about run (default: FALSE)

Value

NULL - results written to file

VCCRI/scTalk documentation built on June 5, 2021, 6:35 a.m.