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Matching_with_DrugTargets/grep_drug_targets.Rmd

+---
+title: "Matching Footprint-based analysis results to harmonised Drug-Targets"
+author: "Alberto Valdeolivas: alvadeolivas@gmail.com; Date:"
+date: "04/04/2022"
+always_allow_html: true
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+### License Info
+
+This program is free software: you can redistribute it and/or modify it under 
+the terms of the GNU General Public License as published by the Free Software 
+Foundation, either version 3 of the License, or (at your option) any later 
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY 
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR 
+A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+Please check http://www.gnu.org/licenses/.
+
+
+# Introduction
+
+The present script takes the output of our Footprint-based analysis and matches
+the results againts a file containing an harmonised list  of drug-targets from DrugBank, 
+clinical trials and also INDRA and AILANI results. 
+
+```{r, warning=FALSE, message=FALSE}
+library(DT)
+library(dplyr)
+```
+
+# Results
+
+## Reading Input files
+
+We first read the harmonised list of drug-target interactions
+
+```{r, warning=FALSE, message=FALSE}
+drug_target <- read.delim("InputFiles/harmonised_drugs_mirnas_ups.tsv")
+```
+
+We then read the output of our Footprint-based analyisis, namely CARNIVAL's output network. 
+This file can be found [here](https://gitlab.lcsb.uni.lu/computational-modelling-and-simulation/footprint-based-analysis-and-causal-network-contextualisation-in-sars-cov-2-infected-a549-cell-line/-/tree/master/Carnival_Results). 
+
+```{r, warning=FALSE, message=FALSE}
+carnival_results <- readRDS("InputFiles/carnival_results_withprogeny.rds")
+carnival_nodes_hgnc <- unique(c(carnival_results$weightedSIF[,"Node1"], carnival_results$weightedSIF[,"Node2"]))
+```
+
+## Matching the results
+
+We finally match all our genes from the carnival network with all the genes from the different pathways
+included in the COVID19 Disease maps.
+
+```{r, warning=FALSE, message=FALSE}
+match_drug_target <- drug_target %>% 
+  dplyr::filter(target_symbol %in% carnival_nodes_hgnc)
+```
+
+and We visualize the results. 
+
+```{r, warning=FALSE, message=FALSE}
+datatable(match_drug_target)
+```
+
+```{r, warning=FALSE, message=FALSE}
+write.table(x=match_drug_target, file = "MatchingDrugs/carnival_drugs.tsv", sep = "\t",
+  row.names = FALSE, quote = FALSE)
+```
+
+# Session Info Details
+
+```{r, echo=FALSE, eval=TRUE}
+sessionInfo()
+```
+
+