Package: prioGene 1.0.1
prioGene: Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
In gene sequencing methods, the topological features of protein-protein interaction (PPI) networks are often used, such as ToppNet <https://toppgene.cchmc.org>. In this study, a candidate gene prioritization method was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease PPI networks with weights for nodes and edges based on functional information.
Authors:
prioGene_1.0.1.tar.gz
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prioGene_1.0.1.tgz(r-4.4-any)prioGene_1.0.1.tgz(r-4.3-any)
prioGene_1.0.1.tar.gz(r-4.5-noble)prioGene_1.0.1.tar.gz(r-4.4-noble)
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prioGene.pdf |prioGene.html✨
prioGene/json (API)
NEWS
| # Install 'prioGene' in R: |
| install.packages('prioGene', repos = c('https://huerqiang.r-universe.dev', 'https://cloud.r-project.org')) |
- R_0 - The vector of initial disease risk scores for all genes
- dise_gene - A vector of disease related genes
- edge_weight - Weights of edges of a net
- genes_mat - A one-to-many matrix of GO term and gene
- metabolic_net - A matrix, Human metabolic network
- net - A network of genes
- net_disease - A network of disease related genes
- net_disease_term - GO terms for each pair of nodes in the network
- node_weight - A matrix, genes and their weights
- terms_mat - A matrix, GO terms and GO genes
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
graphandnetworkfunctionalgenomicsgeneticsnetwork
Last updated 5 years agofrom:13b2a6a503. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 13 2024 |
| R-4.5-win | OK | Nov 13 2024 |
| R-4.5-linux | WARNING | Nov 13 2024 |
| R-4.4-win | OK | Nov 13 2024 |
| R-4.4-mac | OK | Nov 13 2024 |
| R-4.3-win | OK | Nov 13 2024 |
| R-4.3-mac | OK | Nov 13 2024 |
Exports:deal_netget_edge_weightget_gene_matget_net_disease_termget_node_weightget_Rget_R_0get_term_mat
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6rlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Title deal with network | deal_net |
| a vector of disease related genes | dise_gene |
| weights of edges of a net | edge_weight |
| a one-to-many matrix of GO term and gene | genes_mat |
| Title weight edge | get_edge_weight |
| Get a one-to-many matrix of gene and GO term | get_gene_mat |
| Title get neighbor of a node | get_neighbor |
| Title Get the GO terms for each pair of nodes in the network | get_net_disease_term |
| Title weight node | get_node_weight |
| Title get the disease risk transition probability matrix | get_Q |
| Title get the final genetic disease risk scores | get_R |
| Title get the vector of initial disease risk scores for all genes | get_R_0 |
| Get a one-to-many matrix of GO term and gene | get_term_mat |
| Title | get_W |
| a matrix, Human metabolic network | metabolic_net |
| a network of genes | net |
| a network of disease related genes | net_disease |
| GO terms for each pair of nodes in the network | net_disease_term |
| a matrix, genes and their weights | node_weight |
| the vector of initial disease risk scores for all genes | R_0 |
| a matrix, GO terms and GO genes | terms_mat |
