Package: SNPRelate 1.39.0

Xiuwen Zheng

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

Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls in whole-genome and whole-exome variant data.

Authors:Xiuwen Zheng [aut, cre, cph], Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths]

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SNPRelate.pdf |SNPRelate.html✨
SNPRelate/json (API)
NEWS

# Install 'SNPRelate' in R:
install.packages('SNPRelate', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/zhengxwen/snprelate/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:SNPRelate-1.39.0(bioc 3.20)SNPRelate-1.38.0(bioc 3.19)

bioconductor-package

60 exports 3.38 score 1 dependencies 18 dependents 204 mentions 160 downloads

Last updated 2 months agofrom:9da19abc0c

Exports:snpgdsAdmixPlotsnpgdsAdmixPropsnpgdsAdmixTablesnpgdsAlleleSwitchsnpgdsApartSelectionsnpgdsBED2GDSsnpgdsClosesnpgdsCombineGenosnpgdsCreateGenosnpgdsCreateGenoSetsnpgdsCutTreesnpgdsDisssnpgdsDrawTreesnpgdsEIGMIXsnpgdsErrMsgsnpgdsExampleFileNamesnpgdsFstsnpgdsGDS2BEDsnpgdsGDS2EigensnpgdsGDS2PEDsnpgdsGEN2GDSsnpgdsGetGenosnpgdsGRMsnpgdsHClustersnpgdsHWEsnpgdsIBDKINGsnpgdsIBDMLEsnpgdsIBDMLELogLiksnpgdsIBDMoMsnpgdsIBDSelectionsnpgdsIBSsnpgdsIBSNumsnpgdsIndInbsnpgdsIndInbCoefsnpgdsIndivBetasnpgdsIndivBetaRelsnpgdsLDMatsnpgdsLDpairsnpgdsLDpruningsnpgdsMergeGRMsnpgdsOpensnpgdsOptionsnpgdsPairIBDsnpgdsPairIBDMLELogLiksnpgdsPairScoresnpgdsPCAsnpgdsPCACorrsnpgdsPCASampLoadingsnpgdsPCASNPLoadingsnpgdsPED2GDSsnpgdsSampMissRatesnpgdsSelectSNPsnpgdsSlidingWindowsnpgdsSNPListsnpgdsSNPListIntersectsnpgdsSNPRateFreqsnpgdsSummarysnpgdsTransposesnpgdsVCF2GDSsnpgdsVCF2GDS_R

Dependencies:gdsfmt

Tutorials for the R/Bioconductor Package SNPRelate

Xiuwen Zheng (Department of Biostatistics, University of Washington -- Seattle)

Rendered fromSNPRelate.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-07-15
Started: 2019-10-14

Readme and manuals

Help Manual

Help pageTopics
Parallel Computing Toolset for Genome-Wide Association StudiesSNPRelate-package SNPRelate
SNP genotypes of HapMap sampleshapmap_geno
Plot Ancestry ProportionssnpgdsAdmixPlot snpgdsAdmixTable
Estimate ancestral proportions from the eigen-analysissnpgdsAdmixProp
Allele-switchingsnpgdsAlleleSwitch
Select SNPs with a basepair distancesnpgdsApartSelection
Conversion from PLINK BED to GDSsnpgdsBED2GDS
Close the SNP GDS FilesnpgdsClose
Merge SNP datasetssnpgdsCombineGeno
Create a SNP genotype dataset from a matrixsnpgdsCreateGeno
Create a SNP genotype dataset from a GDS filesnpgdsCreateGenoSet
Determine clusters of individualssnpgdsCutTree
Individual dissimilarity analysissnpgdsDiss
Draw a dendrogramsnpgdsDrawTree
Eigen-analysis on SNP genotype dataplot.snpgdsEigMixClass snpgdsEIGMIX
Get the last error informationsnpgdsErrMsg
Example GDS filesnpgdsExampleFileName
SNPGDSFileClassSNPGDSFileClass SNPGDSFileClass-class
F-statistics (fixation indices)snpgdsFst
Conversion from GDS to PLINK BEDsnpgdsGDS2BED
Conversion from GDS to Eigen (EIGENSTRAT)snpgdsGDS2Eigen
Conversion from GDS to PEDsnpgdsGDS2PED
Conversion from Oxford GEN format to GDSsnpgdsGEN2GDS
To get a genotype matrixsnpgdsGetGeno
Genetic Relationship Matrix (GRM) for SNP genotype datasnpgdsGRM
Hierarchical cluster analysissnpgdsHCluster
Statistical test of Hardy-Weinberg EquilibriumsnpgdsHWE
KING method of moment for the identity-by-descent (IBD) analysissnpgdsIBDKING
Maximum likelihood estimation (MLE) for the Identity-By-Descent (IBD) AnalysissnpgdsIBDMLE
Log likelihood for MLE method in the Identity-By-Descent (IBD) AnalysissnpgdsIBDMLELogLik
PLINK method of moment (MoM) for the Identity-By-Descent (IBD) AnalysissnpgdsIBDMoM
Get a table of IBD coefficientssnpgdsIBDSelection
Identity-By-State (IBS) proportionsnpgdsIBS
Identity-By-State (IBS)snpgdsIBSNum
Individual Inbreeding CoefficientssnpgdsIndInb
Individual Inbreeding CoefficientsnpgdsIndInbCoef
Individual inbreeding and relatedness estimation (beta estimator)snpgdsIndivBeta snpgdsIndivBetaRel
Linkage Disequilibrium (LD) analysissnpgdsLDMat
Linkage Disequilibrium (LD)snpgdsLDpair
Linkage Disequilibrium (LD) based SNP pruningsnpgdsLDpruning
Merge Multiple Genetic Relationship Matrices (GRM)snpgdsMergeGRM
Open a SNP GDS FilesnpgdsOpen
Option settings: chromosome coding, etcsnpgdsOption
Calculate Identity-By-Descent (IBD) CoefficientssnpgdsPairIBD
Log likelihood for MLE method in the Identity-By-Descent (IBD) AnalysissnpgdsPairIBDMLELogLik
Genotype Score for Pairs of IndividualssnpgdsPairScore
Principal Component Analysis (PCA) on SNP genotype dataplot.snpgdsPCAClass snpgdsPCA
PC-correlated SNPs in principal component analysissnpgdsPCACorr
Project individuals onto existing principal component axessnpgdsPCASampLoading
SNP loadings in principal component analysissnpgdsPCASNPLoading
Conversion from PLINK PED to GDSsnpgdsPED2GDS
Missing Rate of SamplessnpgdsSampMissRate
SNP selectionsnpgdsSelectSNP
Sliding windowsnpgdsSlidingWindow
Create a SNP list objectsnpgdsSNPList
the class of a SNP listsnpgdsSNPListClass
Get a common SNP list between/among SNP list objectssnpgdsSNPListIntersect
Allele Frequency, Minor Allele Frequency, Missing Rate of SNPssnpgdsSNPRateFreq
Summary of GDS genotype filesnpgdsSummary
Transpose genotypic matrixsnpgdsTranspose
Reformat VCF file(s)snpgdsVCF2GDS
Reformat a VCF file (R implementation)snpgdsVCF2GDS_R