### 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](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).
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)
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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