See DataDescription for the description of data used in the analysis and TablesAndFigures for results description and tables & figures reproduction of the paper. All the haplotype construction and genomic prediction in the paper can be reproduced via scripts in Rscripts and with the Data (please contact authors for some large files).
00-01_DataDescription.Rmd: Rmarkdown for Description of the genotypic and phenotypic data.
00-02_CVSamples.R: Sampling for cross-validation of genomic predcition.
01-01_FixedHB_construction.R: RScript for FixedHB haplotype construction.
01-02_HaploView_construction.R: RScript for HaploView haplotype construction. Should be implemented with shellscript 01-02_Run_HaploView.sh.
01-03_HaploBlocker_construction.R: RScript for HaploBlocker haplotype construction.
02-02_CrossValidation_WeightedGBLUP.R RScript for demonstration of weighting the haplotype length in genomic relationship matrix.
02-01_CrossValidation_GBLUP.R: RScript for haplotype-based genomic prediction for all three scenario.
03-01_TablesAndFigures.Rmd: Rmarkdown for source code of the tables and figures.
Yan-Cheng Lin