# Analysis of Massive SNP Arrays

## Documentation for package ‘bigsnpr’ version 1.4.4

- DESCRIPTION file.

## Help Pages

bigsnpr-package | bigsnpr: Analysis of Massive SNP Arrays
bed | Class bed
bed-class | Class bed
bed-methods | Methods for the bed class
bed_autoSVD | Truncated SVD while limiting LD
bed_clumping | LD clumping
bed_counts | Counts
bed_cprodVec | Cross-product with a vector
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
bigSNP | Class bigSNP
bigSNP-class | Class bigSNP
bigsnpr | bigsnpr: Analysis of Massive SNP Arrays
CODE_012 | CODE_012: code genotype calls (3) and missing values.
CODE_DOSAGE | CODE_012: code genotype calls (3) and missing values.
CODE_IMPUTE_PRED | CODE_012: code genotype calls (3) and missing values.
coef_to_liab | Liability scale
dim-method | Methods for the bed class
download_1000G | Download 1000G
download_beagle | Download Beagle 4.1
download_plink | Download PLINK
download_plink2 | Download PLINK
LD.wiki34 | Long-range LD regions
length-method | Methods for the bed class
same_ref | Determine reference divergence
SCT | Stacked C+T (SCT)
seq_log | Sequence, evenly spaced on a logarithmic scale
snp_asGeneticPos | Interpolate to genetic positions
snp_assocBGEN | Compute quick association statistics from BGEN files
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
snp_fastImpute | Fast imputation
snp_fastImputeSimple | Fast imputation
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_ldpred2_auto | LDpred2
snp_ldpred2_grid | LDpred2
snp_ldpred2_inf | LDpred2
snp_ldsc | LD score regression
snp_ldsc2 | LD score regression
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_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_scaleBinom | Binomial(n, p) scaling
snp_simuPheno | Simulate phenotypes
snp_split | Split-parApply-Combine
snp_subset | Subset a bigSNP
snp_writeBed | Write PLINK files from a "bigSNP"
subset.bigSNP | Subset a bigSNP
sub_bed | Replace extension '.bed'