Repository containing line data and code to produce Table 2 and Figure 1 of the article Hillen et al. (2022). Rituximab and Pyoderma Gangrenosum. An investigation of risk disproportionality using a systems biology-informed approach in the FAERS Database..
The following steps will allow you to run analyse_ritux_pg.R to reproduce Table 2 and Figure 1 of
Hillen et al. (2022):
- Make sure you have R and RStudio installed.
- Download the
ritux_pg.zipfile (on the repo page: greenCodebutton->Download ZIPbutton). - Unzip the download.
- Double click the
ritux_pg.Rprojfile - this should open an RStudio session. - (only has to be performed once) Make sure the prerequisite packages are installed by running the below command in the R console:
install.packages(
c(
"arrow", "dplyr", "tibble",
"ggplot2", "knitr", "tidyr"
)
)
# install pharmsignal package from github
# NOTE: devtools package needs to be installed - please see
# https://www.r-project.org/nosvn/pandoc/devtools.html
devtools::install_github('tystan/pharmsignal')- Now the code is ready to be run:
- Open the
analyse_ritux_pg.Rfile by clicking onFilestab in theFiles/Plots/Packages/...pane of RStudio. - Now to finally run the code in
analyse_ritux_pg.Rin the R console.
- Open the
Table 2: Signal detection estimates and 95% confidence intervals (RSIC = 2^IC using BCPNN MCMC) of rituximab v other comparators for pyoderma gangrenosum
|Comparator | N ritux and PG| N ritux| N comparator and PG| N comparator|RSIC = 2^IC |Potential signal |
|:----------|--------------:|-------:|-------------------:|------------:|:------------------|:----------------|
|(1) All | 32| 30329| 1073| 7741798|6.75 (4.66, 9.21) |* |
|(2) mAbs | 32| 30329| 576| 612437|1.11 (0.77, 1.51) | |
|(3) CD20s | 32| 30329| 3| 17091|1.42 (1.24, 1.53) | |
|(4) RA | 10| 8882| 165| 628285|3.57 (1.78, 5.95) |* |
|(5) MS | 4| 867| 10| 377964|8.46 (2.55, 17.77) |* |
|(6) NHL | 9| 8640| 8| 34407|2.43 (1.38, 3.50) |* |
Figure 1: Signal detection estimates and 95% confidence intervals (RSIC = 2^IC using BCPNN MCMC) of rituximab v other comparators for pyoderma gangrenosum.
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