centrality_score: Node centrality scores for the tissue-specific efficacy...

In vittoriofortino84/ThETA: Transcriptome-based efficacy estimates of target(gene)-disease associations

Description

Three node centrality scores are measured (node degree, clustering coefficient and betweenness) for each tissue-specific network. The networks are built by combining tissue-specific gene expression profiles (which are obtained from GTEx; https://gtexportal.org/) and the human protein-protein interaction (which is obtained from StringDB; https://string-db.org/). The Borda method is used to merge the three ndoe centrality scores. These scores are finally discretized by replacing the rank values with discrete levels of node centrality: 0.25, 0.5, 0.75 and 1.

Usage

data(centrality_score)

Format

A list containing node centrality scores.

Details

It is a list of 4 items: - scores: three centrality scores compiled for each <gene, tissue> pair (list of matrices with genes on the rows and scores on the columns); - ranks: node rankings (list of matrices with genes on the rows and ranks on the columns); - borda: the borda count merging the node rankings (a matrix with genes on the rows and the borda-based rank on the columns/tissues); - borda: a list of discretized borda counts for each tissue.

References

\insertRef

Failli2019ThETA

Examples

data(centrality_score)
names(centrality_score)
head(centrality_score$scores[[1]])
table(centrality_score$borda.disc[[1]])

vittoriofortino84/ThETA documentation built on May 23, 2021, 4:24 a.m.