| Type: | Package |
| Title: | Estimation of Cell Infiltration Based on Cell Crosstalk |
| Version: | 0.1.2 |
| Maintainer: | Junwei Han <hanjunwei1981@163.com> |
| 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. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| LazyData: | true |
| Depends: | R (≥ 2.10) |
| Imports: | fastmatch, igraph, parallel, stats |
| RoxygenNote: | 7.3.2 |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2024-11-08 11:12:22 UTC; 89800 |
| Author: | Junwei Han [aut, cre, cph], Xilong Zhao [aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-11-08 12:20:02 UTC |
CITMIC
Description
The function "CITMIC" is used to identify cell infiltration in tumor microenvironment by calculating intercellular crosstalk.
Usage
CITMIC(GEP,weighted = TRUE,base = 10,damping=0.90,cl.cores=1,cell.type=NULL)
Arguments
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.) |
Value
A data frame containing the cell infiltration score for each sample.
Examples
# 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)
An environment variable that includes some example data
Description
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.
Usage
CITMIC_Data
Format
An environment variable
GetData_CITMIC
Description
Get the example data
Usage
GetData_CITMIC(Data)
Arguments
Data |
A character should be one of "GEP", "matrix_cell_go_inter", "matrix_cell_go_jaccard" |
Value
Data