_pkgdown.yml

url: https://github.com/Alice-MacQueen/switchgrassGWAS/
# url: https://alice-macqueen.github.io/switchgrassGWAS/

reference:
- title: "Datasets"
  desc: "Datasets associated with the pvdiv panel"
- contents:
  - pvdiv_metadata
  - pvdiv_phenotypes
  - anno_info
  - gff_gene
- title: "Genome-wide association"
  desc: "Functions for genome-wide association on the pvdiv panel"
- contents:
  - pvdiv_standard_gwas
  - pvdiv_gwas
  - pvdiv_manhattan
  - pvdiv_qqplot
  - pvdiv_table_topsnps
  - pvdiv_results_in_folder
  - pvdiv_kinship
  - pvdiv_lambda_GC
  - pvdiv_fbm_upset_df
  - pvdiv_fbm_qq
- title: "Multivariate adaptive shrinkage"
  desc: "Functions for multi-condition SNP effect estimates using mash"
- contents:
  - pvdiv_results_in_folder
  - pvdiv_bigsnp2mashr
  - mash_standard_run
  - starts_with("mash")
  - get_colnames
  - get_log10bf
  - get_marker_df
  - get_n_significant_conditions
  - get_significant_results
  - get_estimated_pi
  - get_U_by_mass
  - get_mash_metadata
  - get_GxE
  - get_pairwise_sharing
- title: "Edge-case functions"
  desc: "Additional utility or expert user functions"
- contents:
  - asv_best_PC_df
  - dots
  - get_best_PC_df
  - get_date_filename
  - get_lambdagc
  - get_ncond
  - gff_metadata
  - load_mash_df
  - mt.rawp2adjp
  - pvdiv_autoSVD
  - pvdiv_bigsnp2tibble
  - pvdiv_bigsnp_subset
  - pvdiv_fdr
  - pvdiv_subset_popgenome
  - pvdiv_top_effects_log10p
  - pvdiv_vcf_popgenome
  - reorder_cormat
  - round2
  - round_xy
  - s_hat_bigsnp
  - theme_oeco
  - thresholdFBM