bigSNP-class
Class bigSNP
snp_subset() subset(<bigSNP>)
snp_subset()
subset(<bigSNP>)
Subset a bigSNP
snp_readBed() snp_readBed2()
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
download_plink() download_plink2()
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()
bed_clumping() snp_clumping() snp_pruning() snp_indLRLDR()
bed_clumping()
snp_clumping()
snp_pruning()
snp_indLRLDR()
LD clumping
snp_autoSVD() bed_autoSVD()
snp_autoSVD()
bed_autoSVD()
Truncated SVD while limiting LD
snp_PRS()
PRS
snp_cor()
Correlation matrix
snp_ldsc() snp_ldsc2()
snp_ldsc()
snp_ldsc2()
LD score regression
snp_ldsplit()
Independent LD blocks
snp_match()
Match alleles
snp_grid_clumping() snp_grid_PRS() snp_grid_stacking()
snp_grid_clumping()
snp_grid_PRS()
snp_grid_stacking()
Stacked C+T (SCT)
snp_ldpred2_inf() snp_ldpred2_grid() snp_ldpred2_auto()
snp_ldpred2_inf()
snp_ldpred2_grid()
snp_ldpred2_auto()
LDpred2
snp_thr_correct()
Thresholding and correction
snp_gc()
Genomic Control
snp_qq()
Q-Q plot
snp_manhattan()
Manhattan plot
snp_pcadapt() bed_pcadapt()
snp_pcadapt()
bed_pcadapt()
Outlier detection
snp_MAX3()
MAX3 statistic
snp_fst()
Fixation index (Fst)
snp_asGeneticPos()
Interpolate to genetic positions
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_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
bed()
Class bed
bed_MAF()
Allele frequencies
bed_counts()
Counts
bed_cprodVec()
Cross-product with a vector
bed_prodVec()
Product with a vector
bed_projectPCA()
Projecting PCA
bed_projectSelfPCA()
bed_randomSVD()
Randomized partial SVD
bed_scaleBinom()
Binomial(2, p) scaling
bed_tcrossprodSelf()
Tcrossprod