├── DESCRIPTION ├── NAMESPACE ├── R ├── adm.R ├── fstats.R ├── pca.R └── utils.R ├── doc ├── D.plot.pdf ├── admixture.full.plot.pdf ├── admixture.projected.plot.pdf ├── apx.pca.plot.pdf ├── example.R ├── f3.outgroup.grouped.plot.pdf ├── f3.outgroup.pairs.plot.pdf ├── f3.outgroup.plot.pdf ├── fst.comparison.plot.pdf ├── fst.matrix.plot.pdf ├── fst.nj.plot.pdf └── full.pca.plot.pdf ├── inst └── extdata │ ├── ms.adm.5.P │ ├── ms.adm.5.Q │ ├── ms.adm.5.log │ ├── ms.adm.bed │ ├── ms.adm.bim │ ├── ms.adm.fam │ ├── ms.adm.log │ ├── ms.adm.nosex │ ├── ms.adm.ref.5.P │ ├── ms.adm.ref.5.Q │ ├── ms.adm.ref.5.log │ ├── ms.adm.ref.bed │ ├── ms.adm.ref.bim │ ├── ms.adm.ref.fam │ ├── ms.adm.ref.log │ ├── ms.adm.ref.nosex │ ├── ms.bed │ ├── ms.bim │ ├── ms.fam │ ├── ms.gt.RData │ ├── ms.log │ ├── ms.nosex │ ├── ms.popInfo.RData │ ├── ms.popInfo.txt │ ├── ms.sampleInfo.RData │ ├── ms.sampleInfo.txt │ ├── ms.snpInfo.RData │ ├── plink.log │ └── remove.indlist └── man ├── doAdmixtureProjection.Rd ├── doDTest.Rd ├── doF3Test.Rd ├── fastTable.Rd ├── getAlleleCountsGT.Rd ├── getChromosomeBlocks.Rd ├── getFstAlleleCounts.Rd ├── getFstGT.Rd ├── getPcaGT.Rd ├── getPcaGTFast.Rd ├── llAdmixture.Rd ├── plotAdmixture.Rd ├── plotFPairs.Rd └── plotFStat.Rd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/martinsikora/admixr/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/martinsikora/admixr/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/adm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/martinsikora/admixr/HEAD/R/adm.R -------------------------------------------------------------------------------- /R/fstats.R: 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