pcadapt: Fast Principal Component Analysis for Outlier Detection

Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <DOI:10.1111/1755-0998.12592>.

AuthorKeurcien Luu [aut, cre], Michael Blum [aut], Nicolas Duforet-Frebourg [ctb]
Date of publication2017-01-02 22:22:26
MaintainerKeurcien Luu <keurcien.luu@imag.fr>
LicenseGPL (>= 2)
Version3.0.4

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Files in this package

pcadapt
pcadapt/inst
pcadapt/inst/COPYRIGHTS
pcadapt/inst/extdata
pcadapt/inst/extdata/geno3pops20.zscores
pcadapt/inst/extdata/geno3pops
pcadapt/inst/extdata/geno3pops.maf
pcadapt/inst/extdata/pool3pops
pcadapt/inst/extdata/geno3pops20.loadings
pcadapt/inst/extdata/geno3pops20.maf
pcadapt/inst/extdata/geno3pops.loadings
pcadapt/inst/extdata/geno3pops.scores
pcadapt/inst/extdata/geno3pops.pcadapt
pcadapt/inst/extdata/geno3pops.zscores
pcadapt/inst/extdata/geno3pops.sigma
pcadapt/inst/extdata/geno3pops20.scores
pcadapt/inst/extdata/geno3pops20.sigma
pcadapt/inst/doc
pcadapt/inst/doc/pcadapt.html
pcadapt/inst/doc/pcadapt.R
pcadapt/inst/doc/pcadapt.Rmd
pcadapt/src
pcadapt/src/src_tools
pcadapt/src/src_tools/matrix.c
pcadapt/src/src_tools/linAlgebra.h
pcadapt/src/src_tools/Cov_line.h
pcadapt/src/src_tools/Cov_line.c
pcadapt/src/src_tools/Data__f.h
pcadapt/src/src_tools/random.h
pcadapt/src/src_tools/random.c
pcadapt/src/src_tools/linAlgebra.c
pcadapt/src/src_tools/Data__f.c
pcadapt/src/src_tools/matrix.h
pcadapt/src/pcadapt.h
pcadapt/src/Makevars
pcadapt/src/all2pcadapt.c
pcadapt/src/src_Lapack
pcadapt/src/src_Lapack/dlas2.c
pcadapt/src/src_Lapack/dsyr2k.c
pcadapt/src/src_Lapack/dormql.c
pcadapt/src/src_Lapack/dlarrk.c
pcadapt/src/src_Lapack/dgebrd.c
pcadapt/src/src_Lapack/dlarrf.c
pcadapt/src/src_Lapack/dlaeda.c
pcadapt/src/src_Lapack/dtrsm.c
pcadapt/src/src_Lapack/dlagtf.c
pcadapt/src/src_Lapack/daxpy.c
pcadapt/src/src_Lapack/dlasq6.c
pcadapt/src/src_Lapack/dgebd2.c
pcadapt/src/src_Lapack/dorm2r.c
pcadapt/src/src_Lapack/sysdep1.h
pcadapt/src/src_Lapack/dgelq2.c
pcadapt/src/src_Lapack/dlaed5.c
pcadapt/src/src_Lapack/dlarft.c
pcadapt/src/src_Lapack/fio.h
pcadapt/src/src_Lapack/dtrti2.c
pcadapt/src/src_Lapack/dlabrd.c
pcadapt/src/src_Lapack/dlaed7.c
pcadapt/src/src_Lapack/dlamch.c
pcadapt/src/src_Lapack/dorgqr.c
pcadapt/src/src_Lapack/dormlq.c
pcadapt/src/src_Lapack/dlasd8.c
pcadapt/src/src_Lapack/drotg.c
pcadapt/src/src_Lapack/dbdsdc.c
pcadapt/src/src_Lapack/dsterf.c
pcadapt/src/src_Lapack/dlartg.c
pcadapt/src/src_Lapack/dlacpy.c
pcadapt/src/src_Lapack/dlazq4.c
pcadapt/src/src_Lapack/pow_ii.c
pcadapt/src/src_Lapack/d_sign.c
pcadapt/src/src_Lapack/dlaed2.c
pcadapt/src/src_Lapack/dsytd2.c
pcadapt/src/src_Lapack/dgetrf.c
pcadapt/src/src_Lapack/dlasd2.c
pcadapt/src/src_Lapack/dcopy.c
pcadapt/src/src_Lapack/ddot.c
pcadapt/src/src_Lapack/dlarrc.c
pcadapt/src/src_Lapack/dlarrv.c
pcadapt/src/src_Lapack/dlarfg.c
pcadapt/src/src_Lapack/dgeqrf.c
pcadapt/src/src_Lapack/dorm2l.c
pcadapt/src/src_Lapack/disnan.c
pcadapt/src/src_Lapack/dlaed1.c
pcadapt/src/src_Lapack/dlasd5.c
pcadapt/src/src_Lapack/dorg2l.c
pcadapt/src/src_Lapack/dstebz.c
pcadapt/src/src_Lapack/dlaev2.c
pcadapt/src/src_Lapack/dlasdq.c
pcadapt/src/src_Lapack/s_cat.c
pcadapt/src/src_Lapack/lpk.h
pcadapt/src/src_Lapack/dlasrt.c
pcadapt/src/src_Lapack/clapack.h
pcadapt/src/src_Lapack/dorgl2.c
pcadapt/src/src_Lapack/dnrm2.c
pcadapt/src/src_Lapack/dtrmv.c
pcadapt/src/src_Lapack/ilaenv.c
pcadapt/src/src_Lapack/dlaruv.c
pcadapt/src/src_Lapack/dlapy2.c
pcadapt/src/src_Lapack/dlaed0.c
pcadapt/src/src_Lapack/dlaset.c
pcadapt/src/src_Lapack/dlazq3.c
pcadapt/src/src_Lapack/dorgql.c
pcadapt/src/src_Lapack/dlarrj.c
pcadapt/src/src_Lapack/s_cmp.c
pcadapt/src/src_Lapack/dgemmlig.c
pcadapt/src/src_Lapack/iparmq.c
pcadapt/src/src_Lapack/dlarrb.c
pcadapt/src/src_Lapack/dormbr.c
pcadapt/src/src_Lapack/dlarre.c
pcadapt/src/src_Lapack/dtrmm.c
pcadapt/src/src_Lapack/dsyr2.c
pcadapt/src/src_Lapack/dgesdd.c
pcadapt/src/src_Lapack/dlaed8.c
pcadapt/src/src_Lapack/dgetf2.c
pcadapt/src/src_Lapack/lsame.c
pcadapt/src/src_Lapack/dlaed9.c
pcadapt/src/src_Lapack/dswap.c
pcadapt/src/src_Lapack/dbdsqr.c
pcadapt/src/src_Lapack/dlasd4.c
pcadapt/src/src_Lapack/dlasd1.c
pcadapt/src/src_Lapack/dlasdt.c
pcadapt/src/src_Lapack/dscal.c
pcadapt/src/src_Lapack/pow_di.c
pcadapt/src/src_Lapack/f2c.h
pcadapt/src/src_Lapack/dlaebz.c
pcadapt/src/src_Lapack/dlaisnan.c
pcadapt/src/src_Lapack/pow_dd.c
pcadapt/src/src_Lapack/idamax.c
pcadapt/src/src_Lapack/dlasd7.c
pcadapt/src/src_Lapack/drot.c
pcadapt/src/src_Lapack/dlasr.c
pcadapt/src/src_Lapack/dlassq.c
pcadapt/src/src_Lapack/dormtr.c
pcadapt/src/src_Lapack/dstedc.c
pcadapt/src/src_Lapack/dlasv2.c
pcadapt/src/src_Lapack/dgetrs.c
pcadapt/src/src_Lapack/dlansy.c
pcadapt/src/src_Lapack/dlascl.c
pcadapt/src/src_Lapack/dlaed6.c
pcadapt/src/src_Lapack/dstemr.c
pcadapt/src/src_Lapack/dorml2.c
pcadapt/src/src_Lapack/s_copy.c
pcadapt/src/src_Lapack/dgemv.c
pcadapt/src/src_Lapack/dlasda.c
pcadapt/src/src_Lapack/dgebal.c
pcadapt/src/src_Lapack/dlange.c
pcadapt/src/src_Lapack/i_nint.c
pcadapt/src/src_Lapack/dsymv.c
pcadapt/src/src_Lapack/dlaneg.c
pcadapt/src/src_Lapack/dtrtri.c
pcadapt/src/src_Lapack/dorglq.c
pcadapt/src/src_Lapack/dlasd3.c
pcadapt/src/src_Lapack/dsyevr.c
pcadapt/src/src_Lapack/dger.c
pcadapt/src/src_Lapack/dorgbr.c
pcadapt/src/src_Lapack/dlaed4.c
pcadapt/src/src_Lapack/dgeqr2.c
pcadapt/src/src_Lapack/dorg2r.c
pcadapt/src/src_Lapack/dlarfb.c
pcadapt/src/src_Lapack/dsteqr.c
pcadapt/src/src_Lapack/dormqr.c
pcadapt/src/src_Lapack/dorgtr.c
pcadapt/src/src_Lapack/dgesvd.c
pcadapt/src/src_Lapack/dsytrd.c
pcadapt/src/src_Lapack/dgemm.c
pcadapt/src/src_Lapack/ieeeck.c
pcadapt/src/src_Lapack/dlamrg.c
pcadapt/src/src_Lapack/dlarnv.c
pcadapt/src/src_Lapack/dlasd6.c
pcadapt/src/src_Lapack/dlarrd.c
pcadapt/src/src_Lapack/blaswrap.h
pcadapt/src/src_Lapack/dlarra.c
pcadapt/src/src_Lapack/dstein.c
pcadapt/src/src_Lapack/dlaswp.c
pcadapt/src/src_Lapack/dlasq1.c
pcadapt/src/src_Lapack/dlanst.c
pcadapt/src/src_Lapack/xerbla.c
pcadapt/src/src_Lapack/dlarrr.c
pcadapt/src/src_Lapack/dlar1v.c
pcadapt/src/src_Lapack/dsvdc.c
pcadapt/src/src_Lapack/dlarf.c
pcadapt/src/src_Lapack/dlasq2.c
pcadapt/src/src_Lapack/dgetri.c
pcadapt/src/src_Lapack/dasum.c
pcadapt/src/src_Lapack/dlaed3.c
pcadapt/src/src_Lapack/dlasd0.c
pcadapt/src/src_Lapack/dlasq5.c
pcadapt/src/src_Lapack/dgelqf.c
pcadapt/src/src_Lapack/dlae2.c
pcadapt/src/src_Lapack/dlatrd.c
pcadapt/src/src_Lapack/dlagts.c
pcadapt/src/pcadapt.c
pcadapt/src/src_convert
pcadapt/src/src_convert/ancestrymap.c
pcadapt/src/src_convert/io_tools.c
pcadapt/src/src_convert/geno.h
pcadapt/src/src_convert/ped.c
pcadapt/src/src_convert/io_error.h
pcadapt/src/src_convert/geno.c
pcadapt/src/src_convert/error_matrix.h
pcadapt/src/src_convert/io_data_int.c
pcadapt/src/src_convert/register_convert.h
pcadapt/src/src_convert/io_data_int.h
pcadapt/src/src_convert/read.h
pcadapt/src/src_convert/error_matrix.c
pcadapt/src/src_convert/ancestrymap.h
pcadapt/src/src_convert/ped.h
pcadapt/src/src_convert/io_data_double.h
pcadapt/src/src_convert/io_data_double.c
pcadapt/src/src_convert/io_tools.h
pcadapt/src/src_convert/io_error.c
pcadapt/src/src_convert/io_data_float.c
pcadapt/src/src_convert/register_convert.c
pcadapt/src/src_convert/vcf2geno.h
pcadapt/src/src_convert/io_data_float.h
pcadapt/src/src_convert/vcf2geno.c
pcadapt/src/all2pcadapt.h
pcadapt/src/Makevars.win
pcadapt/NAMESPACE
pcadapt/R
pcadapt/R/pcadaptUtils.R pcadapt/R/pcadaptggPlotting.R pcadapt/R/poolUtils.R pcadapt/R/pcadaptClass.R pcadapt/R/pcadapt.R pcadapt/R/pcadaptPool.R
pcadapt/vignettes
pcadapt/vignettes/pcadapt.Rmd
pcadapt/README.md
pcadapt/MD5
pcadapt/build
pcadapt/build/vignette.rds
pcadapt/DESCRIPTION
pcadapt/man
pcadapt/man/pvalqq.plotting.Rd pcadapt/man/sample.geno.Rd pcadapt/man/cover.to.pool.Rd pcadapt/man/compute.pval.Rd pcadapt/man/manhattan.plotting.Rd pcadapt/man/score.plotting.Rd pcadapt/man/get.pc.Rd pcadapt/man/create.pcadapt.pool.Rd pcadapt/man/read.pcadapt.Rd pcadapt/man/pcadapt-package.Rd pcadapt/man/get.score.color.Rd pcadapt/man/corpca.Rd pcadapt/man/get.pop.names.Rd pcadapt/man/create.pcadapt.Rd pcadapt/man/plot.pcadapt.Rd pcadapt/man/neutral.plotting.Rd pcadapt/man/vcf2pcadapt.Rd pcadapt/man/get.pool.matrix.Rd pcadapt/man/scree.plotting.Rd pcadapt/man/pcadapt.Rd pcadapt/man/convert.line.Rd

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