inter_network: inter network

In SCA-IRCM/SingleCellSignalR: Cell Signalling Using Single Cell RNAseq Data Analysis

inter network

Description

Computes intercellular gene networks.

Usage

inter_network(
  data,
  genes,
  cluster,
  signal,
  c.names = NULL,
  species = c("homo sapiens", "mus musculus"),
  write = TRUE,
  plot = FALSE,
  verbose = TRUE
)

Arguments

data	a data frame of n rows (genes) and m columns (cells) of read or UMI counts (note : rownames(data)=genes)
genes	a character vector of HUGO official gene symbols of length n
cluster	a numeric vector of length m
signal	a list (result of the **cell_signaling()** function)
c.names	(optional) cluster names
species	"homo sapiens" or "mus musculus"
write	a logical (if TRUE writes graphML and text files for the interface and internal networks)
plot	a logical
verbose	a logical

Details

'signal' is a list containing the cell-cell interaction tables. It is the result of the **cell_signaling()** function.

If the user does not set 'c.names', the clusters will be named from 1 to the maximum number of clusters (cluster 1, cluster 2, ...). The user can exploit the 'c.names' vector in the list returned by the **cell_classifier()** function for this purpose. The user can also provide her own cluster names.

'species' must be equal to "homo sapiens" or "mus musculus". In the case of mouse data, the function converts mouse genes in human orthologs (according to Ensembl) such that the Reactome/KEGG interaction database can be exploited, and finally output genes are converted back to mouse.

If 'write' is TRUE, then the function writes four different files. A graphML file in the *cell-signaling* folder for intercellular interactions between each pair of clusters named "intercell_network_Z~1~-Z~2~.graphml", where Z~1~ and Z~2~ are the *c.names* of the clusters. A graphML file in the *cell-signaling* folder that contains a compilation of all the intercellular, ligand-receptor interactions named "full-intercellular-network.graphml". A text and a graphML file in the *networks* folder containing the intracellular network for each cell cluster named "intracell_network_Z.txt" and "intracell_network_Z.graphml", where Z is the *c.names* of the cluster.

Value

The function returns a list containing the tables of interaction between two cell types and the table for the full network of all the cell types.

Examples

m <- data.frame(cell.1=runif(10,0,2),cell.2=runif(10,0,2),cell.3=runif(10,0,2),
cell.4 <- runif(10,0,2),cell.5=runif(10,0,2),cell.6=runif(10,0,2),cell.7=
runif(10,0,2))
rownames(m) <- paste("gene", seq_len(10))
cluster <- c(1,1,1,2,3,3,2)
inter_network(m,rownames(m),cluster,signal=NULL)

SCA-IRCM/SingleCellSignalR documentation built on Dec. 11, 2022, 2:30 p.m.