Skip to content

Latest commit

 

History

History
55 lines (40 loc) · 2.79 KB

README.md

File metadata and controls

55 lines (40 loc) · 2.79 KB
Raw

ritux_pg

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..

How to run code

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.zip file (on the repo page: green Code button -> Download ZIP button).
  • Unzip the download.
  • Double click the ritux_pg.Rproj file - 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.R file by clicking on Files tab in the Files/Plots/Packages/... pane of RStudio.
    • Now to finally run the code in analyse_ritux_pg.R in the R console.

Code outputs: Table 2 and Figure 1

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.