pcadapt: Fast Principal Component Analysis for Outlier Detection

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Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis.

Author
Keurcien Luu, Michael G.B. Blum, Nicolas Duforet-Frebourg
Date of publication
2016-11-03 18:56:15
Maintainer
Keurcien Luu <keurcien.luu@imag.fr>
License
GPL (>= 2)
Version
3.0.3

View on CRAN

Man pages

compute.pval
Principal Components p-values
convert.line
Convert genotype information obtained with vcfR
corpca
Principal Component Analysis based on the correlation matrix
create.pcadapt
pcadapt objects
create.pcadapt.pool
pcadapt objects
get.pc
Get the principal component the most associated with a...
get.pop.names
Retrieve population names
get.score.color
Population colorization
manhattan.plotting
Manhattan Plot
neutral.plotting
Neutral Distribution Estimation
pcadapt
Principal Component Analysis for outlier detection
pcadapt-package
Principal Component Analysis for Outlier Detection.
plot.pcadapt
pcadapt visualization tool
pvalqq.plotting
p-values Q-Q Plot
read.pcadapt
File Converter
score.plotting
Principal Components Analysis Scores Plot
scree.plotting
Principal Components Analysis Scree Plot
vcf2pcadapt
vcfR-based converter

Files in this package

pcadapt
pcadapt/inst
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/poolseq.R
pcadapt/inst/doc/poolseq.html
pcadapt/inst/doc/pcadapt.html
pcadapt/inst/doc/pcadapt.R
pcadapt/inst/doc/pcadapt.Rmd
pcadapt/inst/doc/poolseq.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/pcadaptClass.R
pcadapt/R/pcadapt.R
pcadapt/R/pcadaptPool.R
pcadapt/vignettes
pcadapt/vignettes/pcadapt.Rmd
pcadapt/vignettes/poolseq.Rmd
pcadapt/MD5
pcadapt/build
pcadapt/build/vignette.rds
pcadapt/DESCRIPTION
pcadapt/man
pcadapt/man/pvalqq.plotting.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/scree.plotting.Rd
pcadapt/man/pcadapt.Rd
pcadapt/man/convert.line.Rd