Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)


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Documentation for package ‘SNPRelate’ version 0.9.19

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SNPRelate-package Parallel Computing Toolset for genome-wide association studies
hapmap_geno SNP genotypes of HapMap samples
snpgdsBED2GDS Conversion from PLINK BED to GDS
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
snpgdsErrMsg Get the last error information
snpgdsExampleFileName Example GDS file
snpgdsGDS2BED Conversion from GDS to PLINK BED
snpgdsGDS2Eigen Conversion from GDS to Eigen (EIGENSTRAT)
snpgdsGDS2PED Conversion from GDS to PED
snpgdsGetGeno To get a genotype matrix
snpgdsHCluster Hierarchical cluster analysis
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 The numbers of Identity-By-State (IBS) SNPs
snpgdsIndInb Individual Inbreeding Coefficients
snpgdsIndInbCoef Individual Inbreeding Coefficient
snpgdsLDMat Linkage Disequilibrium (LD) analysis
snpgdsLDpair Linkage Disequilibrium (LD)
snpgdsLDpruning Linkage Disequilibrium (LD) based SNP pruning
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
snpgdsPCA Principal Component Analysis (PCA) on SNP genotype data
snpgdsPCACorr SNP correlation in principal component analysis
snpgdsPCASampLoading Project individuals onto existing principal component axes
snpgdsPCASNPLoading SNP loadings in principal component analysis
snpgdsSampMissrate Missing Rate of Samples
snpgdsSelectSNP SNP selection
snpgdsSNPList Create a SNP list object
snpgdsSNPListClass the class of a SNP list
snpgdsSNPListIntersect Get a common SNP list between two SNP list objects
snpgdsSNPListStrand Switch allele strand.
snpgdsSNPRateFreq Allele Frequency, Minor Allele Frequency, Missing Rate of SNPs
snpgdsSummary Summary of GDS genotype file
snpgdsVCF2GDS Reformat a VCF file
SNPRelate Parallel Computing Toolset for genome-wide association studies