| Title: | Estimation of Cell Infiltration Based on Cell Crosstalk |
|---|---|
| Description: | A systematic biology tool was developed to identify cell infiltration via an Individualized Cell crosstalk network. 'CITMIC' first constructed a weighted cell crosstalk network by integrating Cell-target interaction information, biological process data from the Gene Ontology (GO) database, and gene transcriptomic data in a specific sample, and then, it used a network propagation algorithm on the network to identify cell infiltration for the sample. Ultimately, cell infiltration in the patient dataset was obtained by normalizing the centrality scores of the cells. |
| Authors: | Junwei Han [aut, cre, cph], Xilong Zhao [aut] |
| Maintainer: | Junwei Han <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.1.1 |
| Built: | 2024-10-28 05:06:19 UTC |
| Source: | https://github.com/hanjunwei-lab/citmic |
The function "CITMIC" is used to identify cell infiltration in tumor microenvironment by calculating intercellular crosstalk.
CITMIC(GEP,weighted = TRUE,base = 10,damping=0.90,cl.cores=1,cell.type=NULL)CITMIC(GEP,weighted = TRUE,base = 10,damping=0.90,cl.cores=1,cell.type=NULL)
GEP |
An example gene expression profile. |
weighted |
This parameter specifies whether to create a weighted graph for the cell crosstalk network. If null, an unweighted graph is created, and the elements of the adjacency matrix indicate the number of edges between vertices. If true, a weighted graph is created(default: TRUE). |
base |
Standardized log base of data for improving data distribution(default: 10). |
damping |
Restart the probability of the random-walk algorithm (default: 0.9). |
cl.cores |
The number of CPU cores applied to this task(default:1). |
cell.type |
Preset the relevant cell type (e.g. if the solid tumour tissue does not contain 'HSC', it is better to remove it when we preset it.) |
A data frame containing the cell infiltration score for each sample.
# Obtain the example data GEP<-GetData_CITMIC("GEP") # Run the function lnScore<-CITMIC(GEP,weighted = TRUE,base = 10,damping=0.90,cl.cores=1,cell.type=NULL)# Obtain the example data GEP<-GetData_CITMIC("GEP") # Run the function lnScore<-CITMIC(GEP,weighted = TRUE,base = 10,damping=0.90,cl.cores=1,cell.type=NULL)
matirx_cell_go_inter:A matrix of Jaccard score between cells and GOBP. matirx_cell_go_jaccard:A matrix consisting of genes shared by cells targets and GOBP. GEP:An example gene expression profile.
CITMIC_DataCITMIC_Data
An environment variable
Get the example data
GetData_CITMIC(Data)GetData_CITMIC(Data)
Data |
A character should be one of "GEP", "matrix_cell_go_inter", "matrix_cell_go_jaccard" |
Data