# Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

## Documentation for package ‘SNPRelate’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SNPRelate-package | Parallel Computing Toolset for Genome-Wide Association Studies
hapmap_geno | SNP genotypes of HapMap samples
plot.snpgdsEigMixClass | Eigen-analysis on SNP genotype data
plot.snpgdsPCAClass | Principal Component Analysis (PCA) on SNP genotype data
snpgdsAdmixPlot | Plot Ancestry Proportions
snpgdsAdmixProp | Estimate ancestral proportions from the eigen-analysis
snpgdsAdmixTable | Plot Ancestry Proportions
snpgdsAlleleSwitch | Allele-switching
snpgdsApartSelection | Select SNPs with a basepair distance
snpgdsBED2GDS | Conversion from PLINK BED to GDS
snpgdsClose | Close the SNP GDS File
snpgdsCombineGeno | Merge SNP datasets
snpgdsCreateGeno | Create a SNP genotype dataset from a matrix
snpgdsCreateGenoSet | Create a SNP genotype dataset from a GDS file
snpgdsCutTree | Determine clusters of individuals
snpgdsDiss | Individual dissimilarity analysis
snpgdsDrawTree | Draw a dendrogram
snpgdsEIGMIX | Eigen-analysis on SNP genotype data
snpgdsErrMsg | Get the last error information
snpgdsExampleFileName | Example GDS file
SNPGDSFileClass | SNPGDSFileClass
SNPGDSFileClass-class | SNPGDSFileClass
snpgdsFst | F-statistics (fixation indices)
snpgdsGDS2BED | Conversion from GDS to PLINK BED
snpgdsGDS2Eigen | Conversion from GDS to Eigen (EIGENSTRAT)
snpgdsGDS2PED | Conversion from GDS to PED
snpgdsGEN2GDS | Conversion from Oxford GEN format to GDS
snpgdsGetGeno | To get a genotype matrix
snpgdsGRM | Genetic Relationship Matrix (GRM) for SNP genotype data
snpgdsHCluster | Hierarchical cluster analysis
snpgdsHWE | Statistical test of Hardy-Weinberg Equilibrium
snpgdsIBDKING | KING method of moment for the identity-by-descent (IBD) analysis
snpgdsIBDMLE | Maximum likelihood estimation (MLE) for the Identity-By-Descent (IBD) Analysis
snpgdsIBDMLELogLik | Log likelihood for MLE method in the Identity-By-Descent (IBD) Analysis
snpgdsIBDMoM | PLINK method of moment (MoM) for the Identity-By-Descent (IBD) Analysis
snpgdsIBDSelection | Get a table of IBD coefficients
snpgdsIBS | Identity-By-State (IBS) proportion
snpgdsIBSNum | Identity-By-State (IBS)
snpgdsIndInb | Individual Inbreeding Coefficients
snpgdsIndInbCoef | Individual Inbreeding Coefficient
snpgdsIndivBeta | Individual inbreeding and relatedness estimation (beta estimator)
snpgdsIndivBetaRel | Individual inbreeding and relatedness estimation (beta estimator)
snpgdsLDMat | Linkage Disequilibrium (LD) analysis
snpgdsLDpair | Linkage Disequilibrium (LD)
snpgdsLDpruning | Linkage Disequilibrium (LD) based SNP pruning
snpgdsMergeGRM | Merge Multiple Genetic Relationship Matrices (GRM)
snpgdsOpen | Open a SNP GDS File
snpgdsOption | Option settings: chromosome coding, etc
snpgdsPairIBD | Calculate Identity-By-Descent (IBD) Coefficients
snpgdsPairIBDMLELogLik | Log likelihood for MLE method in the Identity-By-Descent (IBD) Analysis
snpgdsPairScore | Genotype Score for Pairs of Individuals
snpgdsPCA | Principal Component Analysis (PCA) on SNP genotype data
snpgdsPCACorr | PC-correlated SNPs in principal component analysis
snpgdsPCASampLoading | Project individuals onto existing principal component axes
snpgdsPCASNPLoading | SNP loadings in principal component analysis
snpgdsPED2GDS | Conversion from PLINK PED to GDS
snpgdsSampMissRate | Missing Rate of Samples
snpgdsSelectSNP | SNP selection
snpgdsSlidingWindow | Sliding window
snpgdsSNPList | Create a SNP list object
snpgdsSNPListClass | the class of a SNP list
snpgdsSNPListIntersect | Get a common SNP list between/among SNP list objects
snpgdsSNPRateFreq | Allele Frequency, Minor Allele Frequency, Missing Rate of SNPs
snpgdsSummary | Summary of GDS genotype file
snpgdsTranspose | Transpose genotypic matrix
snpgdsVCF2GDS | Reformat VCF file(s)
snpgdsVCF2GDS_R | Reformat a VCF file (R implementation)
SNPRelate | Parallel Computing Toolset for Genome-Wide Association Studies