jdreyf / screendmt-dihome-replication

Data analysis to reproduce results from biorxiv paper

screendmt-dihome-replication

Data, analysis code, and results from Dreyfuss et al. (2024).

Download

1. Click on the green icon "Clone or download" then "Download ZIP"
2. Unzip

Prerequisites

1. Download and Install R: https://cran.r-project.org/
2. Download and Install RStudio Desktop: https://rstudio.com/products/rstudio/download/
3. On Windows, you should have Rtools.

Lipidomics analysis

1. Open the main document here, analyze_screendmt_dihome_replication.Rmd, in R Studio
2. Install and load necessary R packages, including ours such as DirectionalMaxPTest.
   • If asked "Do you want to install from sources the package which needs compilation?" say "no".
3. You can execute the R code in this file in blocks, or you can execute the entire file, including text, to produce an HTML file of the same name using the R Studio button "Knit". This will load our data from the data folder. It then applies our and other packages to our data to reproduce the analyses from the paper.
4. You can compare the results to those at https://github.com/jdreyf/screendmt-dihome-replication/tree/main/results.

Simulations

1. Open simulations_screendmt.Rmd in R Studio
2. Install and load necessary R packages, including ours such as DirectionalMaxPTest.
   • If asked "Do you want to install from sources the package which needs compilation?" say "no".
3. You can execute the R code in this file in blocks, or you can execute the entire file, including text, to produce an HTML file of the same name using the R Studio button "Knit". However, this is very slow.
4. You can see the simulation results for FDR by opening pwr_fdr_arr_b1000_m1000_mu3.5_logpi1.RDS or for FWER by opening pwr_fwer_arr_b1000_m1000_mu3.5_logpi1.RDS in R studio. These are multidimensional arrays that store all simulation results. These reults are plotted in the simulations_screendmt.Rmd chunk ggplot in the Plots section.