Supplementary data and scripts used in the article "Haplotype-based genome wide association study using a novel SNP-set method : RAINBOW"
Author : Kosuke Hamazaki (hamazaki@ut-biomet.org)
Here, I explain the structure of this repository.
HGRAINBOW
data.zip
: This folder contains datasets analyzed in this study. Please download and then decompress.extra
: This folder contain datasets other than genotype and phenotype.Table_S1_origin.csv
: The original data forTable S1
.additive_relationship_matrix.RData
: The additive genetic relationship matrix used in this study.haplotype_block_list.csv
: The list of haplotype block information used in the SNP-set GWAS methods.map2.csv
: The physical map corresponding to the haplotype block list.
genotype
: The marker genotype used in this study.L3024_core_extract_L414_ind1A_ind1B_MAF_0.025_geno.tsv
: The marker genotype of 414 accessions used in this study.L3024_core_extract_L414_ind1A_ind1B_MAF_0.025_haplo1.tsv
: The marker haplotype of 414 accessions used in this study.L3024_core_extract_L414_ind1A_ind1B_MAF_0.025_haplo2.tsv
: The marker haplotype of 414 accessions used in this study.
phenotype
: The phenotypic data simulated in this study.number_of_causals=2_direction_of_effect=minus_trial_no=1.csv
: The phenotypic data for the repulsion scenario.number_of_causals=2_direction_of_effect=plus_trial_no=1.csv
: The phenotypic data for the coupling scenario.seeds_number_of_causals=2_direction_of_effect=minus_trial_no=1.csv
: The random seeds used for simulating phenotypic data for the repulsion scenario.seeds_number_of_causals=2_direction_of_effect=plus_trial_no=1.csv
: The random seeds used for simulating phenotypic data for the coupling scenario.
scripts
: This folder contains scripts with theR
language used in this study.0.0_Rice_HGRAINBOW_subpop_list_to_generate_haplotype_data.R
: Extract subpopulation list from 3,000 accessions.0.1_Rice_HGRAINBOW_haplotype_data.txt
: Extract haplotype data of 414 accessions (plink
andvcftools
) adn estimate haplotype blocks byplink
(notR
!).0.2_Rice_HGRAINBOW_modyfing_haplotype_block_list.R
: Modify haplotype block data estimated byplink
into the format asdata/extra/haplotype_block_list.csv
.0.3_Rice_HGRAINBOW_Simulation_of_phenotypic_values_and_some_preparation.R
: Simulate phenotypic values for both scenarios, coupling and repulsion.0.4_Rice_HGRAINBOW_subpop_list_for_Table_S1.R
: Scripts for generatingTable_S1_origin.csv
.1.1_Rice_HGRAINBOW_score_SKAT_geneset.R
: The function to runSKAT
as haplotype-based GWAS method.1.2_Rice_HGRAINBOW_haplotype_group_fixed_GWAS.R
: The function to runHGF
as haplotype-based GWAS method.1.3_Rice_HGRAINBOW_SS_gwas.R
: The function to calculate summary statistics from GWAS results.2.1_Rice_HGRAINBOW_Haplotype_based_GWAS_for_RAINBOW_package_paper.R
: Perform each GWAS method and save the results.3.1_Rice_HGRAINBOW_Summary_of_HGRAINBOW_Haplotype_based_GWAS_for_RAINBOW.R
: Summary GWAS results.3.2_Rice_HGRAINBOW_Manhattan_plot_from_the_results.R
: Draw Manhattan plots from GWAS results.3.3_Rice_HGRAINBOW_Summary_plot_of_HGRAINBOW_Haplotype_based_GWAS_for_RAINBOW.R
: Draw figures in the article from GWAS results.3.4_Rice_HGRAINBOW_Manhattan_plot_for_overwhelming_results.R
: Draw Manhattan plots for overwhelming results (Figure 4
).