_pkgdown.yml

templates:
  params:
    bootswatch: readable

navbar:
  title: "bigsnpr"
  left:
    - text: "Manual"
      href: reference/index.html
    - text: "Vignettes"
      menu:
      - text: "Quick demo"
        href: articles/demo.html
      - text: "Exercise"
        href: articles/exo.html
      - text: "Why clumping should be preferred over pruning"
        href: articles/pruning-vs-clumping.html
      - text: "How to capture Population Structure with PCA (LD problem explained)"
        href: articles/how-to-PCA.html
      - text: "How to capture Population Structure with PCA (directly on PLINK bed files)"
        href: articles/bedpca.html
      - text: "Ancestry proportions and ancestry grouping"
        href: articles/ancestry.html
      - text: "Computing polygenic scores using Stacked Clumping and Thresholding (SCT)"
        href: articles/SCT.html
      - text: "Polygenic scores and inference using LDpred2"
        href: articles/LDpred2.html
      - text: "Estimating uncertainty in polygenic scores using LDpred2"
        href: articles/prs_uncertainty.html
  right:
    - text: "About"
      icon: fa-user
      href: https://privefl.github.io/about.html
    - icon: fa-github fa
      href: https://github.com/privefl/bigsnpr
    - icon: fa-newspaper-o fa
      href: news/index.html

reference:
  - title: "Class bigSNP"
    contents:
      - bigSNP-class
      - snp_subset
  - title: "I/O"
    contents:
      - snp_readBed
      - snp_readBed2
      - snp_writeBed
      - snp_readBGEN
      - snp_readBGI
      - snp_attach
      - snp_attachExtdata
  - title: "QC / relatedness / imputation"
    contents:
      - download_plink
      - download_plink2
      - download_1000G
      - snp_plinkQC
      - snp_plinkKINGQC
      - snp_plinkIBDQC
      - snp_plinkRmSamples
      - download_beagle
      - snp_beagleImpute
      - snp_fastImpute
      - snp_fastImputeSimple
  - title: "Pruning / correlation"
    contents:
      - snp_pruning
      - snp_clumping
      - snp_indLRLDR
      - snp_autoSVD
      - snp_cor
      - snp_ld_scores
      - snp_ldsc
      - snp_ldsplit
      - LD.wiki34
  - title: "Polygenic scores"
    contents:
      - snp_match
      - snp_grid_clumping
      - snp_grid_PRS
      - snp_grid_stacking
      - snp_ldpred2_inf
      - snp_ldpred2_grid
      - snp_ldpred2_auto
      - snp_lassosum2
      - snp_PRS
      - snp_thr_correct
  - title: "Multiple testing - plots"
    contents:
      - snp_gc
      - snp_qq
      - snp_manhattan
      - snp_pcadapt
      - snp_MAX3
      - snp_fst
  - title: "Utilities"
    contents:
      - snp_prodBGEN
      - snp_match
      - snp_asGeneticPos
      - snp_asGeneticPos2
      - snp_ancestry_summary
      - snp_simuPheno
      - snp_modifyBuild
      - snp_split
      - snp_save
      - snp_getSampleInfos
      - snp_MAF
      - snp_scaleBinom
      - same_ref
      - sub_bed
      - seq_log
      - coef_to_liab
  - title: "PLINK bed files"
    contents:
      - bed
      - bed_MAF
      - bed_autoSVD
      - bed_clumping
      - bed_counts
      - bed_cprodVec
      - bed_pcadapt
      - bed_prodVec
      - bed_projectPCA
      - bed_projectSelfPCA
      - bed_randomSVD
      - bed_scaleBinom
      - bed_tcrossprodSelf