Files in Alice-MacQueen/switchgrassGWAS
Genome Wide Association on Panicum virgatum
.Rbuildignore
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/data.R
R/pvdiv_annotation_tables.R
R/pvdiv_bigsnp2mashr.R
R/pvdiv_gwas.R
R/pvdiv_gwas_results.R
R/pvdiv_mash_results.R
R/pvdiv_mash_wrapper.R
R/pvdiv_popgenome.R
R/pvdiv_standard_gwas.R
R/utils-pipe.R
README.Rmd
README.md
_pkgdown.yml
appveyor.yml
data-raw/Pairwise_sharing_Strong_Effects_5000SNPs.rds
data-raw/Pvirgatum_516_v5.1.gene.gff3.gz
data-raw/anno_info.R
data-raw/example_bedfile.R
data-raw/gff_gene.R
data-raw/gff_metadata.R
data-raw/phenotypes.R
data-raw/pvdiv_metadata.R
data-raw/pvdiv_phenotypes.R
data/anno_info.rda
data/gff_gene.rda
data/gff_metadata.rda
data/pvdiv_metadata.rda
data/pvdiv_phenotypes.rda
data/theme_oeco.rda
inst/extdata/Annotation_tables_3_BIOMASS.rds
inst/extdata/Annotation_tables_GWAS_CT.rds
inst/extdata/Ex_Manhattan.png
inst/extdata/Ex_QQ.png
inst/extdata/Ex_Upset.png
inst/extdata/Ex_Upset_1Mb.png
inst/extdata/GWAS_datatable_example_GWAS_CT.rds
inst/extdata/GWAS_significance_thr_log10p_0_CLMB_BIOMASS_vs_KBSM_BIOMASS.png
inst/extdata/GWAS_significance_thr_log10p_0_CLMB_BIOMASS_vs_PKLE_BIOMASS.png
inst/extdata/Pairwise_sharing_Strong_Effects_5000SNPs.rds
inst/extdata/Strong_Effects5000SNPs.rds
inst/extdata/example.bed
inst/extdata/example.bim
inst/extdata/example.fam
inst/extdata/example_bigsnp.bk
inst/extdata/example_bigsnp.rds
man/anno_info.Rd
man/asv_best_PC_df.Rd
man/dots.Rd
man/expand_cov.Rd
man/figures/Ex_Manhattan.png
man/figures/Ex_QQ.png
man/figures/Ex_Upset.png
man/figures/Ex_Upset_1Mb.png
man/figures/GWAS_significance_thr_log10p_0_CLMB_BIOMASS_vs_KBSM_BIOMASS.png
man/figures/GWAS_significance_thr_log10p_0_CLMB_BIOMASS_vs_PKLE_BIOMASS.png
man/figures/README-unnamed-chunk-3-1.png
man/figures/README-unnamed-chunk-4-1.png
man/figures/README-unnamed-chunk-5-1.png
man/figures/README-unnamed-chunk-6-1.png
man/get_GxE.Rd
man/get_U_by_mass.Rd
man/get_best_PC_df.Rd
man/get_colnames.Rd
man/get_date_filename.Rd
man/get_estimated_pi.Rd
man/get_lambdagc.Rd
man/get_log10bf.Rd
man/get_marker_df.Rd
man/get_mash_metadata.Rd
man/get_n_significant_conditions.Rd
man/get_ncond.Rd
man/get_pairwise_sharing.Rd
man/get_significant_results.Rd
man/gff_gene.Rd
man/gff_metadata.Rd
man/load_mash_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/mt.rawp2adjp.Rd
man/pipe.Rd
man/pvdiv_autoSVD.Rd
man/pvdiv_bigsnp2mashr.Rd
man/pvdiv_bigsnp2tibble.Rd
man/pvdiv_bigsnp_subset.Rd
man/pvdiv_fbm_qq.Rd
man/pvdiv_fbm_upset_df.Rd
man/pvdiv_fdr.Rd
man/pvdiv_gwas.Rd
man/pvdiv_kinship.Rd
man/pvdiv_lambda_GC.Rd
man/pvdiv_manhattan.Rd
man/pvdiv_metadata.Rd
man/pvdiv_phenotypes.Rd
man/pvdiv_qqplot.Rd
man/pvdiv_results_in_folder.Rd
man/pvdiv_standard_gwas.Rd
man/pvdiv_subset_popgenome.Rd
man/pvdiv_table_topsnps.Rd
man/pvdiv_top_effects_log10p.Rd
man/pvdiv_vcf_popgenome.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/thresholdFBM.Rd
switchgrassGWAS.Rproj
tests/testthat.R
tests/testthat/test-pvdiv_gwas_results.R
vignettes/.gitignore
vignettes/annotations.Rmd
vignettes/fbm.Rmd
vignettes/gwas.Rmd
vignettes/inputs.Rmd
vignettes/mash.Rmd
