Function reference • bigsnpr

Class bigSNP
`bigSNP-class` `bigSNP`	Class bigSNP
`snp_subset()` `subset(<bigSNP>)`	Subset a bigSNP
I/O
`snp_readBed()` `snp_readBed2()`	Read PLINK files into a "bigSNP"
`snp_writeBed()`	Write PLINK files from a "bigSNP"
`snp_readBGEN()`	Read BGEN files into a "bigSNP"
`snp_readBGI()`	Read variant info from one BGI file
`snp_attach()`	Attach a "bigSNP" from backing files
`snp_attachExtdata()`	Attach a "bigSNP" for examples and tests
QC / relatedness / imputation
`download_plink()` `download_plink2()`	Download PLINK
`download_1000G()`	Download 1000G
`snp_plinkQC()`	Quality Control
`snp_plinkKINGQC()`	Relationship-based pruning
`snp_plinkIBDQC()`	Identity-by-descent
`snp_plinkRmSamples()`	Remove samples
`download_beagle()`	Download Beagle 4.1
`snp_beagleImpute()`	Imputation
`snp_fastImpute()`	Fast imputation
`snp_fastImputeSimple()`	Fast imputation
Pruning / correlation
`bed_clumping()` `snp_clumping()` `snp_pruning()` `snp_indLRLDR()`	LD clumping
`snp_autoSVD()` `bed_autoSVD()`	Truncated SVD while limiting LD
`snp_cor()` `bed_cor()`	Correlation matrix
`snp_ld_scores()` `bed_ld_scores()`	LD scores
`snp_ldsc()` `snp_ldsc2()`	LD score regression
`snp_ldsplit()`	Independent LD blocks
`LD.wiki34`	Long-range LD regions
Polygenic scores
`snp_match()`	Match alleles
`snp_grid_clumping()` `snp_grid_PRS()` `snp_grid_stacking()`	Stacked C+T (SCT)
`snp_ldpred2_inf()` `snp_ldpred2_grid()` `snp_ldpred2_auto()`	LDpred2
`snp_lassosum2()`	lassosum2
`snp_PRS()`	PRS
`snp_thr_correct()`	Thresholding and correction
Multiple testing - plots
`snp_gc()`	Genomic Control
`snp_qq()`	Q-Q plot
`snp_manhattan()`	Manhattan plot
`snp_pcadapt()` `bed_pcadapt()`	Outlier detection
`snp_MAX3()`	MAX3 statistic
`snp_fst()`	Fixation index (Fst)
Utilities
`snp_prodBGEN()`	BGEN matrix product
`snp_match()`	Match alleles
`snp_asGeneticPos()`	Interpolate to genetic positions
`snp_ancestry_summary()`	Estimation of ancestry proportions
`snp_simuPheno()`	Simulate phenotypes
`snp_modifyBuild()`	Modify genome build
`snp_split()`	Split-parApply-Combine
`snp_save()`	Save modifications
`snp_getSampleInfos()`	Get sample information
`snp_MAF()`	MAF
`snp_scaleAlpha()` `snp_scaleBinom()`	Binomial(n, p) scaling
`same_ref()`	Determine reference divergence
`sub_bed()`	Replace extension '.bed'
`seq_log()`	Sequence, evenly spaced on a logarithmic scale
`coef_to_liab()`	Liability scale
PLINK bed files
`bed()`	Class bed
`bed_MAF()`	Allele frequencies
`snp_autoSVD()` `bed_autoSVD()`	Truncated SVD while limiting LD
`bed_clumping()` `snp_clumping()` `snp_pruning()` `snp_indLRLDR()`	LD clumping
`bed_counts()`	Counts
`bed_cprodVec()`	Cross-product with a vector
`snp_pcadapt()` `bed_pcadapt()`	Outlier detection
`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

Reference

Class bigSNP

I/O

QC / relatedness / imputation

Pruning / correlation

Polygenic scores

Multiple testing - plots

Utilities

PLINK bed files