A script which computes the Quaternary Dot Product Scoring Statistic (or simply the Quaternary Statistic) for signed and unsigned causal graphs using the QuaternaryProd R package over the STRINGdb network.
Before running this script, make sure you have QuaternaryProd installed. To install QuaternaryProd, first make sure you have the latest version of Rstudio, R and the devtools package. Second, you can install the package by running the following in R-studio:
library(devtools)
install_github("carltonyfakhry/QuaternaryProd", build_vignettes = TRUE, local = FALSE)
For an introduction to the Quaternary Dot Product Scoring Statistic, please see the Vignette for QuaternaryProd using the following:
browseVignettes("QuaternaryProd")
First, you need to install the fdrtool R package. Second, you need to download the files in this repository and change your directory to where the files have been downloaded. Finally, to execute the script over the e2f3_sig dataset and the STRINGdb network, run the following in your terminal:
Rscript script.R ./string.ents ./string.rels ./e2f3_sig.txt ./e2f3_sig_output.txt
The results will be outputed to e2f3_sig_output.txt. The same script can be executed with the other datasets myc_sig and ras_sig.