Arabidosis data and R statistical analysis code

The 2023 Arabidosis folder includes 5 folders:

"in Silico 1000 resampling" folder includes two folders; one for Population 1, and one for Population 2, each including 24 files. Each file presents the 1000 lists of plant IDs that were randomly sampled to build control groups (listrand), and the corresponding lists of plant IDs selected on the basis of trait values to build the corresponding high (Top) and low (Bot) selection lines, for the strong (20) and weak (60) selection intensities.

“phenotypic and epiril data” includes two csv files; data_pop1 and data_pop2, respectively for population 1 and 2, and a readme txt file that presents the data included in the files.

“scripts R epigenomic selection” includes two R script files: “PCA_arabidopsis”, which includes the R code used to conduct the PCA analysis on epiRIL data and “Arabette_analysis_loop_Epigenotypes_data”, which is used to insert that epigenotype data in the analysis.

“scripts R epigenomic validation” includes nine R scripts used to conduct tests of molecular epigenomic data validation and comparison with existing data from the literature:  “Script 1 Extract 126 markers from BSMAP ouput files and apply methylkit”, “Script 2 Boxplots of the BS signal distribution for the 126 markers and their correspondence to published HMM classification”, “Script 3 Correlation between EM-seq and BS seq_published_data for the 126 markers”, “Script 4 Correlation between the BS signals of EM-seq and WGBS data for the 126markers”, “Script 5 Hierarchical clustering of the epiRILs EM-seq and published epigenomic data”, “cluster and PCA analysis of Col wt vs 24 sequenced epiRILs”, which filenames are self-explanatory. “methylkit_epiRILs_vs_Col_wt_DMCs” was used to use methylkit in order to identify Differentially Methylated Cytosines between epiRILs and in comparison to Col-0. “methylkit_tiles_script” was used to build the tiles in Methylkit. “verif DMR CHG context” was used to verify differentially methylated regions in the CHG context.

“scripts R phenotypic selection” includes four R scripts “Arabette_analysis”, “Arabette_analysis_loop_Phenotypes_data”, “Arabette_analysis_loop_pop1_final”, “Arabette_analysis_loop_pop2_final” that were used to estimate the parameters used for comparing selection treatments, in other words, to estimate means and confidence intervals (“loop” scripts) in population 1 (“pop1” script) and population 2 (“pop2” script)