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_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_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_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' |
[-method |
Accessor methods for class 'bed'. |