R scripts for PERMANOVA, PERMDISP, and cell-stratified bootstrap analyses of soybean responses to salinity and phosphate deficiency

Description

This repository contains the R scripts used for three analyses reported in the associated manuscript: three-factor PERMANOVA, PERMDISP, and cell-stratified nonparametric bootstrap estimation of difference-in-differences effect sizes. The analyses were conducted in R version 4.2.2. The PERMANOVA and PERMDISP analyses used Bray-Curtis dissimilarities with 9,999 permutations. The bootstrap analysis used 5,000 resamples conducted independently within each genotype and treatment combination. Metabolite abundance values were transformed using log2(x + 1), whereas microbial relative abundances were transformed using the arcsine square-root transformation. This repository contains analysis code and documentation only. It does not contain the study input matrices or formal numerical outputs.

Steps to reproduce

1.Install R version 4.2.2. 2.Download the deposited folder and set it as the working directory. 3.Run Rscript install_packages.R to install or verify the required R packages. 4.Prepare the input files according to INPUT_FORMATS.md. 5.Run Rscript run_all.R <input_directory> <output_directory>. 6.The three analysis scripts can also be run separately by specifying the input and output directories as described in README.md.

Institutions

• Yantai Institute of Coastal Zone Research

  Shandong, Yantai

Categories

Licence