pcadapt: Fast Principal Component Analysis for Outlier Detection
Version 3.0.4

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) .

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pcadapt")

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
cover.to.pool: Simulate frequency matrix from genotype and coverage matrices
create.pcadapt: pcadapt objects
create.pcadapt.pool: pcadapt objects
get.pc: Get the principal component the most associated with a...
get.pool.matrix: Convert genotypes to pooled samples
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
sample.geno: Sample genotype matrix from pooled samples
score.plotting: Principal Components Analysis Scores Plot
scree.plotting: Principal Components Analysis Scree Plot
vcf2pcadapt: vcfR-based converter

Functions

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

Files

inst
inst/COPYRIGHTS
inst/extdata
inst/extdata/geno3pops20.zscores
inst/extdata/geno3pops
inst/extdata/geno3pops.maf
inst/extdata/pool3pops
inst/extdata/geno3pops20.loadings
inst/extdata/geno3pops20.maf
inst/extdata/geno3pops.loadings
inst/extdata/geno3pops.scores
inst/extdata/geno3pops.pcadapt
inst/extdata/geno3pops.zscores
inst/extdata/geno3pops.sigma
inst/extdata/geno3pops20.scores
inst/extdata/geno3pops20.sigma
inst/doc
inst/doc/pcadapt.html
inst/doc/pcadapt.R
inst/doc/pcadapt.Rmd
src
src/src_tools
src/src_tools/matrix.c
src/src_tools/linAlgebra.h
src/src_tools/Cov_line.h
src/src_tools/Cov_line.c
src/src_tools/Data__f.h
src/src_tools/random.h
src/src_tools/random.c
src/src_tools/linAlgebra.c
src/src_tools/Data__f.c
src/src_tools/matrix.h
src/pcadapt.h
src/Makevars
src/all2pcadapt.c
src/src_Lapack
src/src_Lapack/dlas2.c
src/src_Lapack/dsyr2k.c
src/src_Lapack/dormql.c
src/src_Lapack/dlarrk.c
src/src_Lapack/dgebrd.c
src/src_Lapack/dlarrf.c
src/src_Lapack/dlaeda.c
src/src_Lapack/dtrsm.c
src/src_Lapack/dlagtf.c
src/src_Lapack/daxpy.c
src/src_Lapack/dlasq6.c
src/src_Lapack/dgebd2.c
src/src_Lapack/dorm2r.c
src/src_Lapack/sysdep1.h
src/src_Lapack/dgelq2.c
src/src_Lapack/dlaed5.c
src/src_Lapack/dlarft.c
src/src_Lapack/fio.h
src/src_Lapack/dtrti2.c
src/src_Lapack/dlabrd.c
src/src_Lapack/dlaed7.c
src/src_Lapack/dlamch.c
src/src_Lapack/dorgqr.c
src/src_Lapack/dormlq.c
src/src_Lapack/dlasd8.c
src/src_Lapack/drotg.c
src/src_Lapack/dbdsdc.c
src/src_Lapack/dsterf.c
src/src_Lapack/dlartg.c
src/src_Lapack/dlacpy.c
src/src_Lapack/dlazq4.c
src/src_Lapack/pow_ii.c
src/src_Lapack/d_sign.c
src/src_Lapack/dlaed2.c
src/src_Lapack/dsytd2.c
src/src_Lapack/dgetrf.c
src/src_Lapack/dlasd2.c
src/src_Lapack/dcopy.c
src/src_Lapack/ddot.c
src/src_Lapack/dlarrc.c
src/src_Lapack/dlarrv.c
src/src_Lapack/dlarfg.c
src/src_Lapack/dgeqrf.c
src/src_Lapack/dorm2l.c
src/src_Lapack/disnan.c
src/src_Lapack/dlaed1.c
src/src_Lapack/dlasd5.c
src/src_Lapack/dorg2l.c
src/src_Lapack/dstebz.c
src/src_Lapack/dlaev2.c
src/src_Lapack/dlasdq.c
src/src_Lapack/s_cat.c
src/src_Lapack/lpk.h
src/src_Lapack/dlasrt.c
src/src_Lapack/clapack.h
src/src_Lapack/dorgl2.c
src/src_Lapack/dnrm2.c
src/src_Lapack/dtrmv.c
src/src_Lapack/ilaenv.c
src/src_Lapack/dlaruv.c
src/src_Lapack/dlapy2.c
src/src_Lapack/dlaed0.c
src/src_Lapack/dlaset.c
src/src_Lapack/dlazq3.c
src/src_Lapack/dorgql.c
src/src_Lapack/dlarrj.c
src/src_Lapack/s_cmp.c
src/src_Lapack/dgemmlig.c
src/src_Lapack/iparmq.c
src/src_Lapack/dlarrb.c
src/src_Lapack/dormbr.c
src/src_Lapack/dlarre.c
src/src_Lapack/dtrmm.c
src/src_Lapack/dsyr2.c
src/src_Lapack/dgesdd.c
src/src_Lapack/dlaed8.c
src/src_Lapack/dgetf2.c
src/src_Lapack/lsame.c
src/src_Lapack/dlaed9.c
src/src_Lapack/dswap.c
src/src_Lapack/dbdsqr.c
src/src_Lapack/dlasd4.c
src/src_Lapack/dlasd1.c
src/src_Lapack/dlasdt.c
src/src_Lapack/dscal.c
src/src_Lapack/pow_di.c
src/src_Lapack/f2c.h
src/src_Lapack/dlaebz.c
src/src_Lapack/dlaisnan.c
src/src_Lapack/pow_dd.c
src/src_Lapack/idamax.c
src/src_Lapack/dlasd7.c
src/src_Lapack/drot.c
src/src_Lapack/dlasr.c
src/src_Lapack/dlassq.c
src/src_Lapack/dormtr.c
src/src_Lapack/dstedc.c
src/src_Lapack/dlasv2.c
src/src_Lapack/dgetrs.c
src/src_Lapack/dlansy.c
src/src_Lapack/dlascl.c
src/src_Lapack/dlaed6.c
src/src_Lapack/dstemr.c
src/src_Lapack/dorml2.c
src/src_Lapack/s_copy.c
src/src_Lapack/dgemv.c
src/src_Lapack/dlasda.c
src/src_Lapack/dgebal.c
src/src_Lapack/dlange.c
src/src_Lapack/i_nint.c
src/src_Lapack/dsymv.c
src/src_Lapack/dlaneg.c
src/src_Lapack/dtrtri.c
src/src_Lapack/dorglq.c
src/src_Lapack/dlasd3.c
src/src_Lapack/dsyevr.c
src/src_Lapack/dger.c
src/src_Lapack/dorgbr.c
src/src_Lapack/dlaed4.c
src/src_Lapack/dgeqr2.c
src/src_Lapack/dorg2r.c
src/src_Lapack/dlarfb.c
src/src_Lapack/dsteqr.c
src/src_Lapack/dormqr.c
src/src_Lapack/dorgtr.c
src/src_Lapack/dgesvd.c
src/src_Lapack/dsytrd.c
src/src_Lapack/dgemm.c
src/src_Lapack/ieeeck.c
src/src_Lapack/dlamrg.c
src/src_Lapack/dlarnv.c
src/src_Lapack/dlasd6.c
src/src_Lapack/dlarrd.c
src/src_Lapack/blaswrap.h
src/src_Lapack/dlarra.c
src/src_Lapack/dstein.c
src/src_Lapack/dlaswp.c
src/src_Lapack/dlasq1.c
src/src_Lapack/dlanst.c
src/src_Lapack/xerbla.c
src/src_Lapack/dlarrr.c
src/src_Lapack/dlar1v.c
src/src_Lapack/dsvdc.c
src/src_Lapack/dlarf.c
src/src_Lapack/dlasq2.c
src/src_Lapack/dgetri.c
src/src_Lapack/dasum.c
src/src_Lapack/dlaed3.c
src/src_Lapack/dlasd0.c
src/src_Lapack/dlasq5.c
src/src_Lapack/dgelqf.c
src/src_Lapack/dlae2.c
src/src_Lapack/dlatrd.c
src/src_Lapack/dlagts.c
src/pcadapt.c
src/src_convert
src/src_convert/ancestrymap.c
src/src_convert/io_tools.c
src/src_convert/geno.h
src/src_convert/ped.c
src/src_convert/io_error.h
src/src_convert/geno.c
src/src_convert/error_matrix.h
src/src_convert/io_data_int.c
src/src_convert/register_convert.h
src/src_convert/io_data_int.h
src/src_convert/read.h
src/src_convert/error_matrix.c
src/src_convert/ancestrymap.h
src/src_convert/ped.h
src/src_convert/io_data_double.h
src/src_convert/io_data_double.c
src/src_convert/io_tools.h
src/src_convert/io_error.c
src/src_convert/io_data_float.c
src/src_convert/register_convert.c
src/src_convert/vcf2geno.h
src/src_convert/io_data_float.h
src/src_convert/vcf2geno.c
src/all2pcadapt.h
src/Makevars.win
NAMESPACE
R
R/pcadaptUtils.R
R/pcadaptggPlotting.R
R/poolUtils.R
R/pcadaptClass.R
R/pcadapt.R
R/pcadaptPool.R
vignettes
vignettes/pcadapt.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/pvalqq.plotting.Rd
man/sample.geno.Rd
man/cover.to.pool.Rd
man/compute.pval.Rd
man/manhattan.plotting.Rd
man/score.plotting.Rd
man/get.pc.Rd
man/create.pcadapt.pool.Rd
man/read.pcadapt.Rd
man/pcadapt-package.Rd
man/get.score.color.Rd
man/corpca.Rd
man/get.pop.names.Rd
man/create.pcadapt.Rd
man/plot.pcadapt.Rd
man/neutral.plotting.Rd
man/vcf2pcadapt.Rd
man/get.pool.matrix.Rd
man/scree.plotting.Rd
man/pcadapt.Rd
man/convert.line.Rd
pcadapt documentation built on May 20, 2017, 4:46 a.m.