# Analysis of Massive SNP Arrays

## Documentation for package ‘bigsnpr’ version 1.12.21

- DESCRIPTION file.
- Package NEWS.

## Help Pages

bed | Class bed
bed-class | Class bed
bed_autoSVD | Truncated SVD while limiting LD
bed_clumping | LD clumping
bed_cor | Correlation matrix
bed_counts | Counts
bed_cprodVec | Cross-product with a vector
bed_ld_scores | LD scores
bed_MAF | Allele frequencies
bed_pcadapt | Outlier detection
bed_prodVec | Product with a vector
bed_projectPCA | Projecting PCA
bed_projectSelfPCA | Projecting PCA
bed_randomSVD | Randomized partial SVD
bed_RC | Class bed
bed_scaleBinom | Binomial(2, p) scaling
bed_tcrossprodSelf | tcrossprod / GRM
bigSNP | Class bigSNP
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
download_plink2 | Download PLINK
LD.wiki34 | Long-range LD regions
same_ref | Determine reference divergence
SCT | Stacked C+T (SCT)
seq_log | Sequence, evenly spaced on a logarithmic scale
snp_ancestry_summary | Estimation of ancestry proportions
snp_asGeneticPos | Interpolate to genetic positions
snp_asGeneticPos2 | Download a genetic map
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_clumping | LD clumping
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_grid_clumping | Stacked C+T (SCT)
snp_grid_PRS | Stacked C+T (SCT)
snp_grid_stacking | Stacked C+T (SCT)
snp_indLRLDR | LD clumping
snp_lassosum2 | lassosum2
snp_ldpred2_auto | LDpred2
snp_ldpred2_grid | LDpred2
snp_ldpred2_inf | LDpred2
snp_ldsc | LD score regression
snp_ldsc2 | LD score regression
snp_ldsplit | Independent LD blocks
snp_ld_scores | LD scores
snp_MAF | MAF
snp_manhattan | Manhattan plot
snp_match | Match alleles
snp_MAX3 | MAX3 statistic
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_projectSelfPCA | Projecting PCA
snp_PRS | PRS
snp_pruning | LD clumping
snp_qq | Q-Q plot
snp_readBed | Read PLINK files into a "bigSNP"
snp_readBed2 | Read PLINK files into a "bigSNP"
snp_readBGEN | Read BGEN files into a "bigSNP"
snp_readBGI | Read variant info from one BGI file
snp_save | Save modifications
snp_scaleAlpha | Binomial(n, p) scaling
snp_scaleBinom | 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"
subset.bigSNP | Subset a bigSNP
sub_bed | Replace extension '.bed'