Repository to reproduce the analyses in Bastide et al. 2022.

Content

• InterspeciesDE.Rproj: R project that can be opened with R Studio for convenience. All the R scripts assume that the working directory is the root directory of the project.

• R_scripts: R scripts to reproduce the simulations and plots. The scripts are numbered in the order that they should be run. Please see the header of each file for more a mode detailed description of each script.

  • 00_construct_rawTable_Sern2018.R: format the raw counts table from Stern et al. 2018. DO NOT RUN.
  • 01_data_format_Stern2018.R: format the data into a usable PhyloCompData object.
  • 02_simulations_Stern2018.R: simulations using parameters drawn from the data.
  • 03_simulations_data_analysis.R: differential expression analysis of the simulated datasets.
  • 04_simulations_data_analysis_results.R: comparisons of the results from various methods on the same simulated datasets.
  • 05_plot_results.R: plot of the results as presented in the manuscript.
  • 06_simulations_data_check.R: check of the data using countsimQC.
  • 07_data_analysis.R: re-analysis of the Crayfish dataset.

• data: data issued from Stern et al. 2018.

  • crayfish.nodelabels.tre: crayfish tree from Stern et al 2018.
  • states.csv: states of each species (sight / no sight), from Stern et al 2018.
  • rawCounts.txt: raw counts table, produced by R_scripts/00_construct_rawTable_Sern2018.R (DO NOT RUN).
  • rawLengths.txt: raw length table, produced by R_scripts/00_construct_rawTable_Sern2018.R (DO NOT RUN).
  • stern2018_cpd.rds: formatted PhyloCompData dataset, produced by R_scripts/01_data_format_Stern2018.R.

• 2021-12-01_simulations_stern2018: some datasets simulated using R_scripts/02_simulations_Stern2018.R, with base parameters (see text).

  • simulation_parameters.RData: all parameters used for the simulations.
  • all_with_lengths_3_0.8_1_countsim_report.html: reports obtained using the package countsimQC on selected simulated datasets.
  • no_tree_alt_uni_NB_with_lengths_3_1_1_1.rds: dataset simulated without the tree, using the NB framework.
  • real_tree_alt_BM_with_lengths_3_0.8_1_1.rds: dataset simulated using the BM on the tree, and the "alt" design.
  • real_tree_bloc_BM_with_lengths_3_0.8_1_1.rds: dataset simulated using the BM on the tree, and the "bloc" design.
  • real_tree_sights_BM_with_lengths_3_0.8_1_1.rds: dataset simulated using the BM on the tree, and the "sight" design.
  • us_star_tree_alt_uni_BM_with_lengths_3_1_1_1.rds: dataset simulated using the BM on a star tree.

• 2021-12-01_2021-12-01_simulations_stern2018_results: selected results from differential analysis on the simulated datasets.

  • full_result_table_1_50.rds: scores of the various differential expression analysis methods applied on the various simulated datasets. Produced by the R script R_scripts/04_simulations_data_analysis_results.R.

• 2022-11-02_2021-12-01_simulations_stern2018_results: results of a more recent run of the analyses, that includes SVA tests.

Requirements

• R. Version 4.0 or later.

• R package compcodeR. To get the exact same version as the one used to run the scripts for the manuscript, the package can be installed from the phylocomp branch of the GitHub repository, using the following command (see e.g. l.22 of script 01_data_format_Stern2018.R):

devtools::install_github("csoneson/compcodeR", ref = "phylocomp")

• R package countsimQC. Version 1.12.0.