BLUEs_pheno_all.csv - Best linear unbiased estimate (BLUE) phenotype data for all accessions in the panel.
| PI | Subpopulation | Cluster | Race | Origin | DTA | PH | GN | GW | GY | FLH | PL | BL |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PI152651 | Caudatum | 4 | 0 | NA | 66 | 146.61 | 1286 | 27.32 | 43.95 | 97 | 14.33333333 | 57.95 |
| PI17548 | Kafir | 2 | 0 | NA | 66 | 214.06 | 1167 | 15.62 | 26.66 | 156.8333333 | 22.83333333 | 83.41666667 |
| PI24969 | Durra | 3 | 0 | NA | 80 | 182.06 | 1319 | 29.92 | 50.86 | 162 | 13.33333333 | 41.83333333 |
| PI329435 | Mixed | 1 | 0 | NA | 80 | 95.5 | 1388 | 15.68 | 30.47 | 65.83333333 | 26 | 72.58333333 |
Ancestry coefficients of five subpopulations calculated using admixture (Alexandre et. al. 2009).
A zip file containing both genotype matrix (-1,0,1 format) and phenotypic BLUEs.
Manuscript for the publication along with supplementary file. The tables are embedded in the manuscript. The figures and equations (MathType) are included in a separate folder inside this folder.
This folder contains ipython notebooks used in computation for this study.
lme4_1.1-21 MCMCglmm_2.29 ape_5.3 coda_0.19-2 Matrix_1.2-17 BGLR_1.0.8 rrBLUP_4.6
This script contains the functions my.read.vcf to read SNP files in vcf format, and the parse.vcf function to create a genotype matrix (in -1,0,1 format) that can be used in the rrBLUP package.
R script to create a cross-validation file with individuals proportionally divided from each cluster into five equal folds.
R scripts used to implement GBLUP and cross validations using kin.blup function in R package rrBLUP.
- CV1_prediction.R # proportional sampling from races
- CV2_AR_prediction.R # sampling from across race
- CV2_WR_prediction.R # sampling from within race
Fits multi-response model in MCMCglmm to calculate variance-covariance components due to conditional expectations from race.
R script to calculate heterozygosity per site using R package Pegas.
Calculations for expected values of R^2 under drift equilibrium Hill and Weir (1988). As implemented in Remington et al. (2001).
Calculates variance components and genomic heritability