The pipeline must be excuted under R base 3.5.1 or higher
In order to correctly charge all the scripts and paths it must we performed in the PIPELINE_TFM_Marina.Rproj All the scripts needed to repropduce the results presented in the TFM "Mechanistic models for drug repositioining in rare diseases" are located in "/scripts", they MUST be executed in their numerated order: 00-01-02-03-04-05
00_librariesPackages.R --> Loads all the packages and libraries needed in this project.
01_DiseaseMapConstruction_Annotation.R --> Builds up the Disease Map from a given KEGGpathwayID(XXXX), i.e. For hsa03460 => KEGGpathID = "03460" and two tabular files containing extra genes and extra interactions named after the KEGGpathID, i.e. For hsa03460 => vertex_03460.xls; edges_03460.xls Annotation of the Disease Map with DrugBank and HPO
02_HPOenrichment_DescriptiveAnalysis.R --> Enrichment analysis of the HPO terms associated to the genes of the Disease Map ; Enrichment of the HPO associated to the Disease-network
03_DataPreparation_preHiPathia.R --> Preprocessment of the genesets chosen: 1.Normalization with RMA of the raw data 2. Tranformation Probe to gene (preprocessment for HiPathia method)
04_HiPathiaMethod_4FAkeggPathway.R --> HiPathia validation Part I: Performance of HiPathia method on previously preproccessed geneset GSEA16334 over Fanconi Anemia KEGG Pathway
05_HiPathiaMethod_4DiseaseMap.R --> HiPathia validation Part II: Performance of HiPathia method on previously preproccessed geneset GSEA16334 over Disease Map (Extended FA Disease pathway)
"/data"
Contains all the tables and data sets needed to carry out the analyses, for downloading:
https://drive.google.com/open?id=12y5PyQXmlwzaXKgnZqGZcpIfX70lMW-O
"/library"
Contains information needed to buld up the new metaginfo for the inclusion of the Disease Map in HiPathia method.
"/OUTPUT"
All the tables and results will be exported to this folder.