Analysis of Massive SNP Arrays


[Up] [Top]

Documentation for package ‘bigsnpr’ version 1.8.1

Help Pages

bigsnpr-package bigsnpr: Analysis of Massive SNP Arrays
bed Class bed
bed-class Class bed
bed-methods Methods for the bed class
bed_autoSVD Truncated SVD while limiting LD
bed_clumping LD clumping
bed_counts Counts
bed_cprodVec Cross-product with a vector
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
bigSNP Class bigSNP
bigSNP-class Class bigSNP
bigsnpr bigsnpr: Analysis of Massive SNP Arrays
CODE_012 CODE_012: code genotype calls (3) and missing values.
CODE_DOSAGE CODE_012: code genotype calls (3) and missing values.
CODE_IMPUTE_PRED CODE_012: code genotype calls (3) and missing values.
coef_to_liab Liability scale
dim-method Methods for the bed class
download_1000G Download 1000G
download_beagle Download Beagle 4.1
download_plink Download PLINK
download_plink2 Download PLINK
LD.wiki34 Long-range LD regions
length-method Methods for the bed class
same_ref Determine reference divergence
SCT Stacked C+T (SCT)
seq_log Sequence, evenly spaced on a logarithmic scale
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_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_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_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'