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_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_PRS()

PRS

snp_cor()

Correlation

Stacked Clumping and Thresholding (SCT)

snp_match()

Match alleles

snp_grid_clumping() snp_grid_PRS() snp_grid_stacking()

Stacked C+T (SCT)

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

Utilities

snp_match()

Match alleles

snp_modifyBuild()

Modify genome build

snp_split()

Split-parApply-Combine

snp_save()

Save modifications

snp_getSampleInfos()

Get sample information

snp_MAF()

MAF

snp_scaleBinom()

Binomial(n, p) scaling

subset(<bigSNP>)

Subset

same_ref()

Determine reference divergence

sub_bed()

Replace extension '.bed'

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