LD.wiki34               Long-range LD regions
SCT                     Stacked C+T (SCT)
bed-class               Class bed
bed_MAF                 Allele frequencies
bed_clumping            LD clumping
bed_counts              Counts
bed_cprodVec            Cross-product with a vector
bed_prodVec             Product with a vector
bed_projectPCA          Projecting PCA
bed_projectSelfPCA      Projecting PCA
bed_randomSVD           Randomized partial SVD
bed_scaleBinom          Binomial(2, p) scaling
bed_tcrossprodSelf      tcrossprod / GRM
bigSNP-class            Class bigSNP
coef_to_liab            Liability scale
download_1000G          Download 1000G
download_beagle         Download Beagle 4.1
download_genetic_map    Download a genetic map
download_plink          Download PLINK
same_ref                Determine reference divergence
seq_log                 Sequence, evenly spaced on a logarithmic scale
snp_MAF                 MAF
snp_MAX3                MAX3 statistic
snp_PRS                 PRS
snp_ancestry_summary    Estimation of ancestry proportions
snp_asGeneticPos        Interpolate to genetic positions
snp_attach              Attach a "bigSNP" from backing files
snp_attachExtdata       Attach a "bigSNP" for examples and tests
snp_autoSVD             Truncated SVD while limiting LD
snp_beagleImpute        Imputation
snp_cor                 Correlation matrix
snp_fastImpute          Fast imputation
snp_fastImputeSimple    Fast imputation
snp_fst                 Fixation index (Fst)
snp_gc                  Genomic Control
snp_getSampleInfos      Get sample information
snp_lassosum2           lassosum2
snp_ld_scores           LD scores
snp_ldpred2_inf         LDpred2
snp_ldsc                LD score regression
snp_ldsplit             Independent LD blocks
snp_manhattan           Manhattan plot
snp_match               Match alleles
snp_modifyBuild         Modify genome build
snp_pcadapt             Outlier detection
snp_plinkIBDQC          Identity-by-descent
snp_plinkKINGQC         Relationship-based pruning
snp_plinkQC             Quality Control
snp_plinkRmSamples      Remove samples
snp_prodBGEN            BGEN matrix product
snp_qq                  Q-Q plot
snp_readBGEN            Read BGEN files into a "bigSNP"
snp_readBGI             Read variant info from one BGI file
snp_readBed             Read PLINK files into a "bigSNP"
snp_save                Save modifications
snp_scaleAlpha          Binomial(n, p) scaling
snp_simuPheno           Simulate phenotypes
snp_split               Split-parApply-Combine
snp_subset              Subset a bigSNP
snp_thr_correct         Thresholding and correction
snp_writeBed            Write PLINK files from a "bigSNP"
sub_bed                 Replace extension '.bed'
