Analysis of Massive SNP Arrays
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Documentation for package ‘bigsnpr’ version 1.12.2
Help Pages
| 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'. |