# barley-agroclimatic-association **Repository Path**: xiekunwhy/barley-agroclimatic-association ## Basic Information - **Project Name**: barley-agroclimatic-association - **Description**: No description available - **Primary Language**: Unknown - **License**: GPL-3.0 - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2020-06-09 - **Last Updated**: 2020-12-19 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README This repository contains data files and source code used in a project in which we looked for genome-wide association with high-resolution climate data of the Iberian Peninsula with the goal of discovering selection footprints in the genomes of barley landraces from the [Spanish Barley Core Collection](http://www.eead.csic.es/barley/index.php?lng=1). URL: [eead-csic-compbio.github.io/barley-agroclimatic-association](https://eead-csic-compbio.github.io/barley-agroclimatic-association) **Authors** B Contreras-Moreira (1,2), R Serrano-Notivoli (1), NE Mohamed (1), CP Cantalapiedra (1), S Begueria (1), AM Casas (1), E Igartua (1) 1. Estacion Experimental de Aula Dei-CSIC, Zaragoza, Spain 2. Fundacion ARAID, Zaragoza, Spain ![**Legend.** Flowchart of the analyses carried out in this work.](./flowchart.png) There are several R markdown documents describing the selection of agroclimatic variables, mapping and diverse protocols for association analyses: | filename | summary | |:---------|:--------:| |[HOWTOclimate](./HOWTOclimate.html)| Preparation and selection of climate variables | |[HOWTOstructure](./HOWTOstructure.html)| Analysis of population structure of Spanish barleys | |[HOWTORDA](./HOWTORDA.html)| Redundancy Analysis | |[HOWTOLD](./HOWTOLD.html)| Linkage Disequilibrium | |[HOWTOsnps](./HOWTOsnps.html)| Association between SNPs and climate variables (Bayenv2) | |[HOWTOsnpsLFMM](./HOWTOsnpsLFMM.html)| Association between SNPs and climate variables (LFMM) | |[HOWTOXtX](./HOWTOXtX.html)| XtX subpopulation differentiation (Bayenv2) | |[HOWTOXtX_BAYPASS](./HOWTOXtX_BAYPASS.html)| XtX subpopulation differentiation (BayPass) | **Data files** The table below describes some data files used in this work. You can find them in the repository, mainly at maps/, and raw/ folders, if you click on [View on GitHub](https://github.com/eead-csic-compbio/barley-agroclimatic-association): | filename | description | |:---------|:-----------:| |[raw/barley_climate_updated.tsv](./raw/barley_climate_updated.tsv) | Values of agro-climatic and environmental variables at the geographical collection points of the barley accessions. | |[raw/barley_climate_pca_scores.tsv](./raw/barley_climate_pca_scores.tsv) | Values of principal components of the agro-climatic and environmental variables at the geographical collection points of the barley accessions. | |[maps/climatologies_5km.RData](./maps/climatologies_5km.RData) | 5x5 km grids of agro-climatic and environmental (lat, lon, alt) variables over Spain, required for producing the maps in [HOWTOclimate](./HOWTOclimate.html). | |[maps/climatologies_5km_pca.RData](./maps/climatologies_5km_pca.RData) | 5x5 km grids of principal components of the agro-climatic and environmental variables over Spain, required for producing the maps in [HOWTOclimate](./HOWTOclimate.html)| |[matrices/SBCCmatrix_nr_mean.txt](./matrices/SBCCmatrix_nr_mean.txt) | Non-redundant covariance matrix obtained by averaging 10 Bayenv2 replicates. | |[raw/SBCC_Kinship.full.tsv](./raw/SBCC_Kinship.full.tsv) | Tab-separated file assigning SBCC landraces to 4 subpopulations. | |[raw/9920_SNPs_SBCC_50K.tsv](./raw/9920_SNPs_SBCC_50K.tsv) | Tab-separated matrix with SBCC biallelic SNPs. | |[raw/9920_SNPs_SBCC_bp_map2017.curated.tsv](./raw/9920_SNPs_SBCC_bp_map2017.curated.tsv) | Tab-separated file with physical positions of SNPs assigned by [BARLEYMAP](http://floresta.eead.csic.es/barleymap) | |[raw/9920_SNPs_SBCC_cM_map2017.curated.tsv](./raw/9920_SNPs_SBCC_cM_map2017.curated.tsv) | Tab-separated file with genetic positions of SNPs assigned by [BARLEYMAP](http://floresta.eead.csic.es/barleymap) | **Bayenv demo** A demo dataset to learn how to run bayenv2 locally is available at [bayenv/BAYENV_EXAMPLE.tgz](./bayenv/BAYENV_EXAMPLE.tgz). It can be downloaded in the terminal with: ``wget https://eead-csic-compbio.github.io/barley-agroclimatic-association/bayenv/BAYENV_EXAMPLE.tgz`` **Downloads** It is possible to get the complete dataset, source code and documentation in two ways: + downloading the release (143MB) [![DOI](https://zenodo.org/badge/138037295.svg)](https://zenodo.org/badge/latestdoi/138037295) + cloning the GitHub repository (783MB) **Dependencies** Besides [bayenv2](https://gcbias.org/bayenv), [LFMM](http://membres-timc.imag.fr/Olivier.Francois/lfmm) and a few Perl scripts, included in this repository, these protocols require a few R packages which must be installed to reproduce the results: [LDcorSV](https://cran.r-project.org/web/packages/LDcorSV/index.html), [ape](https://cran.r-project.org/package=ape), [calibrate](https://cran.r-project.org/package=calibrate), [cluster](https://cran.r-project.org/package=cluster), [corrplot](https://cran.r-project.org/package=corrplot), [dendextend](https://cran.r-project.org/package=dendextend), [devtools](https://cran.r-project.org/package=devtools), [dplyr](https://cran.r-project.org/package=dplyr), [ggplot2](https://cran.r-project.org/package=ggplot2), [gplots](https://cran.r-project.org/package=gplots), [grid](https://cran.r-project.org/package=grid), [knitr](https://cran.r-project.org/package=knitr). [maptools](https://cran.r-project.org/package=maptools), [pracma](https://cran.r-project.org/package=pracma), [qqman](https://cran.r-project.org/package=qqman), [raster](https://cran.r-project.org/package=raster), [vegan](https://cran.r-project.org/package=vegan). The BayPass XtX protocol requires the system installation of [BayPass](http://www1.montpellier.inra.fr/CBGP/software/baypass).