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

View on CRAN

Functions

compute.pval Man page
convert.line Man page
corpca Man page
cover.to.pool Man page
create.pcadapt Man page
create.pcadapt.pool Man page
get.pc Man page
get.pool.matrix Man page
get.pop.names Man page
get.score.color Man page
manhattan.plotting Man page
neutral.plotting Man page
pcadapt Man page
pcadapt-package Man page
plot.pcadapt Man page
pvalqq.plotting Man page
read.pcadapt Man page
sample.geno Man page
score.plotting Man page
scree.plotting Man page
vcf2pcadapt Man page

Files

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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