prioritization_genes: Candidate genes prioritization

In AnaGalhoz37/wppi: Weighting protein-protein interactions

Candidate genes prioritization

Description

Ranks candidate genes based on correlation with the given seed genes of interest. For this, the source proteins/genes (i.e. starting nodes) are reduced to the candidate genes and the target proteins/genes (i.e. end nodes) to the given genes of interest. Each candidate gene score is defined by the sum of its correlations towards the known disease-related genes.

Usage

prioritization_genes(
  graph_op,
  prob_matrix,
  genes_interest,
  percentage_genes_ranked = 100
)

Arguments

graph_op	Igraph object based on OmniPath PPI interactions from graph_from_op.
prob_matrix	Matrix object with correlations/probabilities of the all nodes in the network from random_walk.
genes_interest	Character vector with known-disease specific genes.
percentage_genes_ranked	Positive integer (range between 0 and 100) specifying the percentage ( network returned in the output. If not specified, the score of all the candidate genes is delivered.

Value

Data frame with the ranked candidate genes based on the functional score inferred from given ontology terms, PPI and Random Walk with Restart parameters.

See Also

• graph_from_op

• weighted_adj

• random_walk

• score_candidate_genes_from_PPI

Examples

db <- wppi_data()
GO_data <- db$go
HPO_data <- db$hpo
# Genes of interest
genes_interest <-
    c("ERCC8", "AKT3", "NOL3", "GFI1B", "CDC25A", "TPX2", "SHE")
# Graph object with PPI 
graph_op <- graph_from_op(db$omnipath)
graph_op_1 <- subgraph_op(graph_op, genes_interest, 1)
# Filter ontology data
GO_data_filtered <- filter_annot_with_network(GO_data, graph_op_1)
HPO_data_filtered <- filter_annot_with_network(HPO_data, graph_op_1)
# Weighted adjacency
w_adj <- weighted_adj(graph_op_1, GO_data_filtered, HPO_data_filtered)
# Random Walk with Restart
w_rw <- random_walk(w_adj)
# Ranked candidate genes
scores <- prioritization_genes(graph_op_1, w_rw, genes_interest)

AnaGalhoz37/wppi documentation built on Nov. 8, 2022, 7:47 a.m.