grep_drug_targets.md

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.

library(DT)
library(dplyr)

Results

Reading Input files

We first read the harmonised list of drug-target interactions

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.

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.

match_drug_target <- drug_target %>% 
  dplyr::filter(target_symbol %in% carnival_nodes_hgnc)

and We visualize the results.

datatable(match_drug_target)

write.table(x=match_drug_target, file = "MatchingDrugs/carnival_drugs.tsv", sep = "\t",
  row.names = FALSE, quote = FALSE)

Session Info Details

## R version 4.0.4 (2021-02-15)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_Germany.1252  LC_CTYPE=English_Germany.1252   
## [3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C                    
## [5] LC_TIME=English_Germany.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] dplyr_1.0.8 DT_0.21    
## 
## loaded via a namespace (and not attached):
##  [1] rstudioapi_0.13   knitr_1.33        magrittr_2.0.1    tidyselect_1.1.2 
##  [5] R6_2.5.1          rlang_1.0.1       fansi_1.0.2       stringr_1.4.0    
##  [9] tools_4.0.4       webshot_0.5.2     xfun_0.24         utf8_1.2.2       
## [13] DBI_1.1.2         cli_3.2.0         jquerylib_0.1.4   crosstalk_1.1.1  
## [17] htmltools_0.5.1.1 ellipsis_0.3.2    assertthat_0.2.1  yaml_2.2.1       
## [21] digest_0.6.27     tibble_3.1.6      lifecycle_1.0.1   crayon_1.5.0     
## [25] purrr_0.3.4       sass_0.4.0        htmlwidgets_1.5.3 vctrs_0.3.8      
## [29] glue_1.4.2        evaluate_0.14     rmarkdown_2.9     stringi_1.6.2    
## [33] bslib_0.2.5.1     compiler_4.0.4    pillar_1.7.0      generics_0.1.2   
## [37] jsonlite_1.7.2    pkgconfig_2.0.3