Files in Alice-MacQueen/CDBNgenomics

Genomics Using the Cooperative Dry Bean Nursery Dataset

.Rbuildignore

.gitignore

.travis.yml

CDBNgenomics.Rproj

DESCRIPTION

NAMESPACE

R/GAPIT_PC_selection.R R/cdbn_bigsnp2mashr.R R/cdbn_kinship.R R/data.R R/get_annotations.R R/handle_mash_results.R R/mash_standard_run.R R/utils-pipe.R README.Rmd README.md analysis-paper/ASReml_BLUPs_Figures.Rmd

analysis-paper/BLUP_Descriptive_Statistics.csv

analysis-paper/BLUP_Descriptive_Statistics.xlsx

analysis-paper/BLUP_Descriptive_Statistics_ASReml.xlsx

analysis-paper/BLUPs_analysis.Rmd

analysis-paper/METG_Genetics_2020-01-11.docx

analysis-paper/Make_GAPIT_TopSNP_Tables.R

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.33.24.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.34.04.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.36.01.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.36.43.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.37.18.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.37.53.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.38.29.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.39.28.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.40.08.bmp

analysis-paper/SNPs with significant effects in n conditions 2019-08-07 16.42.40.bmp

analysis-paper/Supplement_Fig_1_ASReml.svg

analysis-paper/To Upload/100 word summary, editors, reviewers.docx

analysis-paper/To Upload/100 word summary.docx

analysis-paper/To Upload/CDBN_METG_Manuscript.zip

analysis-paper/To Upload/Cover Letter.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Comments for Reviewers 2019-12-03.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Comments for Reviewers 2020-01-16.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Comments for Reviewers 2020-01-20.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Comments for Reviewers 2020-01-20_TJ.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Comments for Reviewers 2020-03-11.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Cover Letter March.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Cover Letter.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_1_2020-03-18.pdf

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_1_2020-03-18.svg

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_1_CDBN_GLY.png

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_1_Draft_inkscape_2020-03-18.svg

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_2_Phenotypes_2020-03-18.pdf

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_2_Phenotypes_2020-03-18.svg

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_3_2020-03-18.eps

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_3_2020-03-18.pdf

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_3_mash_2020-01-28.png

analysis-paper/To Upload/Edited_Manuscript_2020/Figure_3_mash_draft_2019-12-10.svg

analysis-paper/To Upload/Edited_Manuscript_2020/METG_Genetics_ASReml.docx

analysis-paper/To Upload/Edited_Manuscript_2020/METG_Genetics_rrBLUP.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Manuscript_proof_ahm.pdf

analysis-paper/To Upload/Edited_Manuscript_2020/Response to Reviewers.docx

analysis-paper/To Upload/Edited_Manuscript_2020/Supporting Information.docx

analysis-paper/To Upload/Edited_Manuscript_2020/mash_effects_S01_15360302_2019-12-10.png

analysis-paper/To Upload/Edited_Manuscript_2020/mash_effects_S01_42228454_2019-12-10.png

analysis-paper/To Upload/Edited_Manuscript_2020/mash_effects_S07_14474325_2019-12-10.png

analysis-paper/To Upload/Edited_Manuscript_2020/~$TG_Genetics_2019-12-02.docx

analysis-paper/To Upload/METG_Genetics_2019-08-08.docx

analysis-paper/To Upload/Supplement_2019-07-10.docx

analysis-paper/To Upload/Supplementary_Table_2_new.xlsx

analysis-paper/To Upload/Supplementary_Table_4_FDR.xlsx

analysis-paper/To Upload/Supplementary_Table_5.xlsx

analysis-paper/Visualize_ASReml_GWAS.R

analysis-paper/mash/B_hat_random_df_4000topSNPs.rds

analysis-paper/mash/B_hat_strong_df_4000topSNPs.rds

analysis-paper/mash/Mash_data_driven_covariances_4000.rds

analysis-paper/mash/Model_of_random_tests_4000SNPs.rds

analysis-paper/mash/Pairwise_sharing_Strong_Effects_4000SNPs.rds

analysis-paper/mash/Pairwise_sharing_sign_Strong_Effects_4000SNPs.rds

analysis-paper/mash/S_hat_random_df_4000topSNPs.rds

analysis-paper/mash/S_hat_strong_df_4000topSNPs.rds

analysis-paper/mash/Strong_Effects4000SNPs.rds

analysis-paper/mash/mash_run_v1.R analysis-paper/mash_22_phenotype_visualization_2019-07-08.Rmd

analysis-paper/mash_22_phenotype_visualization_2019-07-08_files/figure-html/unnamed-chunk-3-1.png

analysis-paper/mash_22_phenotype_visualization_2019-07-08_files/figure-html/unnamed-chunk-5-1.png

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analysis-paper/mash_figure_panel_a.svg

analysis-paper/mash_table_output_BFgt2_2019-07-09.csv

data-raw/ASReml/ASReml_coefficients_13_GAPIT_2020-01-12.txt

data-raw/ASReml/GAPIT-for-mash/10perFDR_annosWithin100kbp_GAPIT_BLUP_PC0_phenotypedonly_2020-01-14.rds

data-raw/ASReml/GAPIT-for-mash/10perFDR_annosWithin100kbp_GAPIT_BLUP_PC0_phenotypedonly_2020-01-17.rds

data-raw/ASReml/GAPIT-for-mash/10perFDR_withAnnotatedSNP_GAPIT_BLUP_PC0_phenotypedonly_2020-01-14.xlsx

data-raw/ASReml/GAPIT-for-mash/10perFDR_withAnnotatedSNP_GAPIT_BLUP_PC0_phenotypedonly_2020-01-17.xlsx

data-raw/ASReml/GAPIT-for-mash/ASReml_BM_Manhattan.png

data-raw/ASReml/GAPIT-for-mash/ASReml_BM_TopSNPEffects.png

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data-raw/ASReml/GAPIT-for-mash/ASReml_Earliest_Year_CDBN_TopSNPEffects.png

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data-raw/ASReml/GAPIT-for-mash/ASReml_ZN_TopSNPEffects.png

data-raw/ASReml/GAPIT-for-mash/All_significant_regions_localscore.rds

data-raw/ASReml/GAPIT-for-mash/All_significant_regions_localscore_ksi3.rds

data-raw/ASReml/GAPIT-for-mash/B_hat_random_df_2200topSNPs.rds

data-raw/ASReml/GAPIT-for-mash/B_hat_random_df_2500topSNPs.rds

data-raw/ASReml/GAPIT-for-mash/B_hat_strong_df_2200topSNPs.rds

data-raw/ASReml/GAPIT-for-mash/B_hat_strong_df_2500topSNPs.rds

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data-raw/ASReml/GAPIT-for-mash/Manhattan_BM_ksi_2_2020-01-16 12.41.27.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_BM_ksi_3_2020-01-17 11.44.38.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_BR_ksi_3_2020-01-17 11.45.17.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_CT_ksi_2_2020-01-16 12.44.29.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_CT_ksi_3_2020-01-17 11.47.15.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_DF_ksi_2_2020-01-16 12.45.13.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_DM_ksi_2_2020-01-16 12.45.57.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_DM_ksi_3_2020-01-17 11.48.33.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_Earliest_Year_CDBN_ksi_2_2020-01-16 12.46.40.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_GH_ksi_2_2020-01-16 12.48.07.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_GH_ksi_3_2020-01-17 11.50.28.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_HB_ksi_2_2020-01-16 12.48.50.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_HB_ksi_3_2020-01-17 11.51.07.png

data-raw/ASReml/GAPIT-for-mash/Manhattan_HI_ksi_2_2020-01-16 12.49.33.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_PH_ksi_2_2020-01-16 12.50.59.png

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data-raw/ASReml/GAPIT-for-mash/Manhattan_RR_ksi_2_2020-01-16 12.51.44.png

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data-raw/ASReml/GAPIT-for-mash/Mash_pairwise_shared_effects_2020-01-16 15.29.50.png

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data-raw/ASReml/GAPIT-for-mash/Model_of_random_tests_2200SNPs.rds

data-raw/ASReml/GAPIT-for-mash/Model_of_random_tests_30114SNPs.rds

data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.BM.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.BR.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.CB.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.CM.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.CT.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.DF.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.DM.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.EV.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.Earliest_Year_CDBN.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.GH.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.HB.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.HI.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.LG.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.PH.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.RR.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.RU.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.SA.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.SF.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.SW.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.SY.Manhattan.Plot.Genomewise.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.SY.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.WM.Optimum.pdf data-raw/ASReml/GAPIT-for-mash/Optimum/GAPIT.CMLM.ZN.Optimum.pdf

data-raw/ASReml/GAPIT-for-mash/Pairwise_sharing_Strong_Effects_2200SNPs.rds

data-raw/ASReml/GAPIT-for-mash/Pairwise_sharing_Strong_Effects_30114SNPs.rds

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data-raw/ASReml/GAPIT-for-mash/Rplots.pdf

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data-raw/ASReml/GAPIT-for-mash/S_hat_random_df_2200topSNPs.rds

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data-raw/ASReml/L_LbY_TbL_TbY/BM_No_Vg_Model_ASReml.rds

data-raw/ASReml/L_LbY_TbL_TbY/BM_No_Vg_Model_Predictions.rds

data-raw/ASReml/L_LbY_TbL_TbY/BR_No_Vg_Model_ASReml.rds

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data-raw/GAPIT-example/EMMA_functions.R data-raw/GAPIT-example/GAPIT_example_code.R data-raw/GAPIT-example/GAPIT_functions.R

data-raw/GAPIT-example/kinBLUP_phenotypedOnly_GAPIT_PC0_2019-02-27.txt

data-raw/GAPIT.Kin.VanRaden.csv

data-raw/GAPIT.PCA.csv

data-raw/GAPIT.PCA.eigenvalues.csv

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr1.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr10.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr11.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr2.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr3.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr4.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr5.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr6.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr7.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr8.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GD_CDBN_001_359_pedigree_fillin_chr9.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr1.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr10.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr11.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr2.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr3.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr4.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr5.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr6.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr7.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr8.txt.gz

data-raw/GAPIT_Numerical_format_files/Numerical_format_GM_CDBN_001_359_pedigree_fillin_chr9.txt.gz

data-raw/Long Range LD METG 2018-10-22.Rmd

data-raw/Pairwise_sharing_Strong_Effects_4000SNPs.rds

data-raw/Pairwise_sharing_sign_Strong_Effects_4000SNPs.rds

data-raw/Pv_GO.R data-raw/Pv_kegg.R

data-raw/Pvulgaris_442_v2.1.gene.sqlite

data-raw/Strong_Effects4000SNPs.rds

data-raw/anno_info.R

data-raw/kinBLUP_phenotypedOnly_GAPIT_2019-02-26.txt

data-raw/metadata.R

data-raw/rsconnect/documents/CDBN_Phenotypes_cleanup_V2.0.Rmd/rpubs.com/rpubs/Document.dcf

data-raw/rsconnect/documents/CDBN_Phenotypes_cleanup_V2.0.Rmd/rpubs.com/rpubs/Publish Document.dcf

data-raw/theme_oeco.R data-raw/txdb.R

data/BLUPs.rda

data/Pv_GO.rda

data/Pv_kegg.rda

data/anno_info.rda

data/metadata.rda

data/theme_oeco.rda

data/txdb.rda

man/BLUPs.Rd man/Pv_GO.Rd man/Pv_kegg.Rd man/anno_info.Rd man/cdbn_bigsnp2mashr.Rd man/cdbn_gwas.Rd man/cdbn_standard_gwas.Rd man/expand_cov.Rd

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man/gapit_model_selection.Rd man/gapit_results_in_filepath.Rd man/get_GxE.Rd man/get_SVD.Rd man/get_U_by_mass.Rd man/get_annotations.Rd man/get_best_PC_df.Rd man/get_colnames.Rd man/get_date_filename.Rd man/get_estimated_pi.Rd man/get_kinship.Rd man/get_lambda_GC.Rd man/get_lambdagc.Rd man/get_log10bf.Rd man/get_marker_df.Rd man/get_n_significant_conditions.Rd man/get_ncond.Rd man/get_pairwise_sharing.Rd man/get_qqplot.Rd man/get_results_in_folder.Rd man/get_significant_results.Rd man/get_top_effects_log10p.Rd man/load_g2m_df.Rd man/mash_plot_Ulist.Rd man/mash_plot_covar.Rd man/mash_plot_effects.Rd man/mash_plot_manhattan_by_condition.Rd man/mash_plot_pairwise_sharing.Rd man/mash_plot_sig_by_condition.Rd man/mash_standard_run.Rd man/metadata.Rd man/pipe.Rd man/reorder_cormat.Rd man/round2.Rd man/round_xy.Rd man/s_hat_bigsnp.Rd man/scale_cov.Rd man/theme_oeco.Rd man/txdb.Rd

Alice-MacQueen/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.m.