PI: Networking Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Version 1.0.0

Priority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging genetic data to prioritise targets at the gene, pathway and network level. Based on evidence of genetic association from GWAS data, this prioritisation system is able to resolve modulated genes (seed genes) by utilising knowledge of linkage disequilibrium (co-inherited variants), distance from the gene, and evidence of genetic association with gene expression. Seed genes are scored in an integrative way quantifying the genetic influence. Scored seed genes are subsequently used as baits to rank seed genes plus additional (non-seed) genes; this is achieved by iteratively exploring the global connectivity of a gene interaction network. Genes with the top priority are further used to identify/prioritise pathways that are significantly enriched with highly prioritised genes. Prioritised genes are also used to identify a gene network interconnecting many highly prioritised genes but a few lowly prioritised genes as linkers.

AuthorHai Fang, the ULTRA-DD consortium, Julian C Knight
Bioconductor views Bioinformatics
Date of publication2016-04-25 09:21:46
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.0.0
URL http://pi314.r-forge.r-project.org
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PI", repos="http://R-Forge.R-project.org")

Popular man pages

xPrioritiser: Function to do prioritisation through random walk techniques
xPrioritiserGenes: Function to priorise genes from an input network and the...
xPrioritiserManhattan: Function to visualise prioritised genes using manhattan plot
xPrioritiserSNPs: Function to priorise genes given a list of seed SNPs together...
xPrioritiserSubnet: Function to identify a gene network from top prioritised...
xRWR: Function to implement Random Walk with Restart (RWR) on the...
xPrioritiserPathways: Function to prioritise pathways based on enrichment analysis...
See all...

All man pages Function index File listing

Man pages

xPrioritiser: Function to do prioritisation through random walk techniques
xPrioritiserGenes: Function to priorise genes from an input network and the...
xPrioritiserManhattan: Function to visualise prioritised genes using manhattan plot
xPrioritiserPathways: Function to prioritise pathways based on enrichment analysis...
xPrioritiserSNPs: Function to priorise genes given a list of seed SNPs together...
xPrioritiserSubnet: Function to identify a gene network from top prioritised...
xRWR: Function to implement Random Walk with Restart (RWR) on the...

Functions

xPrioritiser Man page Source code
xPrioritiserGenes Man page Source code
xPrioritiserManhattan Man page Source code
xPrioritiserPathways Man page Source code
xPrioritiserSNPs Man page Source code
xPrioritiserSubnet Man page Source code
xRWR Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/xPrioritiser.r
R/xPrioritiserGenes.r
R/xPrioritiserManhattan.r
R/xPrioritiserPathways.r
R/xPrioritiserSNPs.r
R/xPrioritiserSubnet.r
R/xRWR.r
inst
inst/AS.txt
inst/NEWS
inst/PI.icon.png
inst/PI.logo.png
inst/SLE.txt
inst/Spondyloarthritis.txt
inst/iAnno.txt
inst/xPrioritiser.html
inst/xPrioritiserGenes.html
inst/xPrioritiserManhattan.html
inst/xPrioritiserPathways.html
inst/xPrioritiserSNPs.html
inst/xPrioritiserSubnet.html
inst/xRWR.html
man
man/xPrioritiser.Rd
man/xPrioritiserGenes.Rd
man/xPrioritiserManhattan.Rd
man/xPrioritiserPathways.Rd
man/xPrioritiserSNPs.Rd
man/xPrioritiserSubnet.Rd
man/xRWR.Rd
PI documentation built on May 21, 2017, 1:24 a.m.

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