node.centrality: Compile Node Centrality Scores For A Given PPI Network.

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

Description

Determine three node centrality measures (node degree, clustering coefficient and betweenness) for a given ppi network.

Usage

node.centrality(
  ppi_network,
  tissue_expr_data,
  agg_function = 4,
  directed_network = F,
  parallel = NULL,
  verbose = FALSE
)

Arguments

ppi_network	a matrix or a data frame with at least two columns reporting the ppi connections (or edges). Each line corresponds to a direct interaction. Columns give the gene IDs of the two interacting proteins. Only interactions whose destination nodes match with the IDs provided in tissue_expr_data will be considered during the computation.
tissue_expr_data	numeric matrix or data frame indicating expression significances in the form of Z-scores. Columns are tissues and rows are genes; colnames and rownames must be provided.
agg_function	integer value between 1 and 4. Provides control over Borda aggregation functions. 1 for mean, 2 for median, 3 for geo.mean and 4 for l2norm. Defaults to 4.
directed_network	boolean value indicating the use of a direct network. Defaults to FALSE.
parallel	an integer indicating how many cores will be registered for parallel computation. If NULL, the function will not use parallel computation.
verbose	logical to indicate whether the messages will be displayed or not in the screen.

Details

The three scores are merged with the Borda method. See \insertRefFailli2019ThETA, for more details.

Value

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.

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