LEA: LEA: an R package for Landscape and Ecological Association Studies

LEA is an R package dedicated to landscape genomics and ecological association tests. LEA can run analyses of population structure and genome scans for local adaptation. It includes statistical methods for estimating ancestry coefficients from large genotypic matrices and evaluating the number of ancestral populations (snmf, pca); and identifying genetic polymorphisms that exhibit high correlation with some environmental gradient or with the variables used as proxies for ecological pressures (lfmm), and controlling the false discovery rate. LEA is mainly based on optimized C programs that can scale with the dimension of very large data sets.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("LEA")
AuthorEric Frichot <eric.frichot@gmail.com>, Olivier Francois <olivier.francois@imag.fr>
Bioconductor views Clustering Regression Software StatisticalMethod
Date of publicationNone
MaintainerEric Frichot <eric.frichot@gmail.com>
LicenseGPL-3
Version1.8.0
http://membres-timc.imag.fr/Olivier.Francois/lea.html

View on Bioconductor

Man pages

adjusted_pvalues: adjusted p-values from a lfmm run

ancestrymap: 'ancestrymap' format description

ancestrymap2geno: Convert from 'ancestrymap' to 'geno' format

ancestrymap2lfmm: Convert from 'ancestrymap' to 'lfmm' format

crossEntropy: Cross-entropy criterion from snmf runs

env: Environmental input file format for 'lfmm'

G: Ancestral allele frequencies from a snmf run

geno: Input file for 'snmf'

geno2lfmm: Convert from 'geno' to 'lfmm' format

lfmm: Input file for 'lfmm'

lfmm2geno: Convert from 'lfmm' to 'geno' format

main_createDataSet: create a data set with masked data

main_crossEntropyEstimation: compute the cross-entropy criterion

main_LFMM: Fitting Latent Factor Mixed Models

main_pca: Principal Component Analysis

main_sNMF: Estimates individual ancestry coefficients and ancestral...

main_tracyWidom: Tracy-Widom test for eigenvalues

mlog10pvalues: -log10(p-values) from a lfmm run

ped: 'ped' format description

ped2geno: Convert from 'ped' to 'geno' format

ped2lfmm: Convert from 'ped' to 'lfmm' format

pvalues: p-values from a lfmm run

Q: Admixture coefficients from a snmf run

readEnv: Read environmental file in the 'env'format

readGeno: read a file in the 'geno' format

readLfmm: Read files in the 'lfmm' format

readZscore: Read the output files of 'lfmm'

Replop-package: LEA: an R package for Landscape and Ecological Associations...

tutorial: Example tutorial data sets

vcf: 'vcf' format description

vcf2geno: Convert from 'vcf' to 'geno' format

vcf2lfmm: Convert from 'vcf' to 'lfmm' format

writeEnv: Write files in the 'env' format

writeGeno: Write files in the 'geno' format

writeLFMM: Write files in the 'lfmm' format

zscore: Output file format for 'lfmm'

zscores: z-scores from a lfmm run

Functions

adjusted.pvalues Man page
adjusted.pvalues,lfmmProject-method Man page
ancestrymap Man page
ancestrymap2geno Man page
ancestrymap2lfmm Man page
combine.lfmmProject Man page
combine.lfmmProject,character,character-method Man page
combine.snmfProject Man page
combine.snmfProject,character,character-method Man page
create.dataset Man page
cross.entropy Man page
cross.entropy.estimation Man page
cross.entropy,snmfProject-method Man page
eigenvalues Man page
eigenvalues,pcaProject-method Man page
eigenvectors Man page
eigenvectors,pcaProject-method Man page
env Man page
example_ancestrymap Man page
example_geno Man page
example_lfmm Man page
example_ped Man page
example_vcf Man page
export.lfmmProject Man page
export.lfmmProject,character-method Man page
export.pcaProject Man page
export.pcaProject,character-method Man page
export.snmfProject Man page
export.snmfProject,character-method Man page
G Man page
geno Man page
geno2lfmm Man page
G,snmfProject-method Man page
import.lfmmProject Man page
import.lfmmProject,character-method Man page
import.pcaProject Man page
import.pcaProject,character-method Man page
import.snmfProject Man page
import.snmfProject,character-method Man page
LEA-package Man page
lfmm Man page
lfmm2geno Man page
lfmm.data Man page
load.lfmmProject Man page
load.lfmmProject,character-method Man page
load.pcaProject Man page
load.pcaProject,character-method Man page
load.snmfProject Man page
load.snmfProject,character-method Man page
mlog10p.values Man page
mlog10p.values,lfmmProject-method Man page
pca Man page
$,pcaProject-method Man page
ped Man page
ped2geno Man page
ped2lfmm Man page
plot,lfmmProject-method Man page
plot,pcaProject-method Man page
plot,snmfProject-method Man page
projections Man page
projections,pcaProject-method Man page
p.values Man page
p.values,lfmmProject-method Man page
Q Man page
Q,snmfProject-method Man page
read.env Man page
read.geno Man page
read.lfmm Man page
read.zscore Man page
remove.lfmmProject Man page
remove.lfmmProject,character-method Man page
remove.pcaProject Man page
remove.pcaProject,character-method Man page
remove.snmfProject Man page
remove.snmfProject,character-method Man page
sdev Man page
sdev,pcaProject-method Man page
show,lfmmClass-method Man page
show,lfmmProject-method Man page
show,pcaProject-method Man page
show,snmfClass-method Man page
show,snmfProject-method Man page
snmf Man page
summary,lfmmProject-method Man page
summary,pcaProject-method Man page
summary,snmfProject-method Man page
tracy.widom Man page
tracy.widom,pcaProject-method Man page
tutorial Man page
vcf Man page
vcf2geno Man page
vcf2lfmm Man page
write.env Man page
write.geno Man page
write.lfmm Man page
zscore.format Man page
z.scores Man page
z.scores,lfmmProject-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/LFMM.R R/ancestrymap2geno.R R/ancestrymap2lfmm.R R/createDataSet.R R/crossEntropyEstimation.R R/geno2lfmm.R R/lfmm2geno.R R/lfmmClass.R R/lfmmProject.R R/pca.R R/pcaProject.R R/ped2geno.R R/ped2lfmm.R R/readEnv.R R/readGeno.R R/readLfmm.R R/readZscore.R R/sNMF.R R/snmfClass.R R/snmfProject.R R/test_character.R R/test_double.R R/test_extension.R R/test_input_file.R R/test_integer.R R/test_logical.R R/tools.R R/vcf2geno.R R/vcf2lfmm.R R/writeEnv.R R/writeGeno.R R/writeLfmm.R
build
build/vignette.rds
data
data/datalist
data/example_ancestrymap.txt.gz
data/example_geno.tab.gz
data/example_lfmm.txt.gz
data/example_ped.txt.gz
data/example_vcf.txt.gz
data/tutorial.RData
inst
inst/CITATION
inst/doc
inst/doc/LEA.R
inst/doc/LEA.Rnw
inst/doc/LEA.pdf
man
man/G.Rd man/Q.Rd man/Replop-package.Rd man/adjusted_pvalues.Rd man/ancestrymap.Rd man/ancestrymap2geno.Rd man/ancestrymap2lfmm.Rd man/crossEntropy.Rd man/env.Rd man/geno.Rd man/geno2lfmm.Rd man/lfmm.Rd man/lfmm2geno.Rd man/main_LFMM.Rd man/main_createDataSet.Rd man/main_crossEntropyEstimation.Rd man/main_pca.Rd man/main_sNMF.Rd man/main_tracyWidom.Rd man/mlog10pvalues.Rd man/ped.Rd man/ped2geno.Rd man/ped2lfmm.Rd man/pvalues.Rd man/readEnv.Rd man/readGeno.Rd man/readLfmm.Rd man/readZscore.Rd man/tutorial.Rd man/vcf.Rd man/vcf2geno.Rd man/vcf2lfmm.Rd man/writeEnv.Rd man/writeGeno.Rd man/writeLFMM.Rd man/zscore.Rd man/zscores.Rd
src
src/LFMM
src/LFMM/LFMM.c
src/LFMM/LFMM.h
src/LFMM/U.c
src/LFMM/U.h
src/LFMM/V.c
src/LFMM/V.h
src/LFMM/beta.c
src/LFMM/beta.h
src/LFMM/beta_k0.c
src/LFMM/beta_k0.h
src/LFMM/data_lfmm.c
src/LFMM/data_lfmm.h
src/LFMM/error_lfmm.c
src/LFMM/error_lfmm.h
src/LFMM/lfmm_algo.c
src/LFMM/lfmm_algo.h
src/LFMM/lfmm_k0.c
src/LFMM/lfmm_k0.h
src/LFMM/print_lfmm.c
src/LFMM/print_lfmm.h
src/LFMM/register_lfmm.c
src/LFMM/register_lfmm.h
src/LFMM/slice_lfmm.c
src/LFMM/slice_lfmm.h
src/LFMM/thread_lfmm.c
src/LFMM/thread_lfmm.h
src/LFMM/thread_var.c
src/LFMM/thread_var.h
src/Makevars
src/Makevars.win
src/R_LFMM.c
src/R_LFMM.h
src/R_ancestrymap2geno.c
src/R_ancestrymap2geno.h
src/R_ancestrymap2lfmm.c
src/R_ancestrymap2lfmm.h
src/R_createDataSet.c
src/R_createDataSet.h
src/R_crossEntropy.c
src/R_crossEntropy.h
src/R_geno2lfmm.c
src/R_geno2lfmm.h
src/R_init_LEA.c
src/R_lfmm2geno.c
src/R_lfmm2geno.h
src/R_pca.c
src/R_pca.h
src/R_ped2geno.c
src/R_ped2geno.h
src/R_ped2lfmm.c
src/R_ped2lfmm.h
src/R_sNMF.c
src/R_sNMF.h
src/R_tracyWidom.c
src/R_tracyWidom.h
src/R_vcf2geno.c
src/R_vcf2geno.h
src/bituint
src/bituint/bituint.c
src/bituint/bituint.h
src/bituint/calc_bituint.c
src/bituint/calc_bituint.h
src/bituint/io_geno_bituint.c
src/bituint/io_geno_bituint.h
src/bituint/slice_bituint.c
src/bituint/slice_bituint.h
src/bituint/thread_bituint.c
src/bituint/thread_bituint.h
src/convert
src/convert/ancestrymap.c
src/convert/ancestrymap.h
src/convert/convert.h
src/convert/geno.c
src/convert/geno.h
src/convert/geno2lfmm.c
src/convert/geno2lfmm.h
src/convert/lfmm2geno.c
src/convert/lfmm2geno.h
src/convert/ped.c
src/convert/ped.h
src/convert/register_convert.c
src/convert/register_convert.h
src/convert/vcf2geno.c
src/convert/vcf2geno.h
src/createDataSet
src/createDataSet/createDataSet.c
src/createDataSet/createDataSet.h
src/createDataSet/error_cds.c
src/createDataSet/error_cds.h
src/createDataSet/print_cds.c
src/createDataSet/print_cds.h
src/createDataSet/register_cds.c
src/createDataSet/register_cds.h
src/crossEntropy
src/crossEntropy/crossEntropy.c
src/crossEntropy/crossEntropy.h
src/crossEntropy/error_ce.c
src/crossEntropy/error_ce.h
src/crossEntropy/print_ce.c
src/crossEntropy/print_ce.h
src/crossEntropy/register_ce.c
src/crossEntropy/register_ce.h
src/io
src/io/io.h
src/io/io_data_double.c
src/io/io_data_double.h
src/io/io_data_float.c
src/io/io_data_float.h
src/io/io_data_int.c
src/io/io_data_int.h
src/io/io_error.c
src/io/io_error.h
src/io/io_tools.c
src/io/io_tools.h
src/io/print_bar.c
src/io/print_bar.h
src/io/read.h
src/matrix
src/matrix/cholesky.c
src/matrix/cholesky.h
src/matrix/data.c
src/matrix/data.h
src/matrix/diagonalize.c
src/matrix/diagonalize.h
src/matrix/error_matrix.c
src/matrix/error_matrix.h
src/matrix/inverse.c
src/matrix/inverse.h
src/matrix/matrix.c
src/matrix/matrix.h
src/matrix/normalize.c
src/matrix/normalize.h
src/matrix/rand.c
src/matrix/rand.h
src/matrix/random_projection.c
src/matrix/random_projection.h
src/matrix/slice_matrix.c
src/matrix/slice_matrix.h
src/matrix/sylvester.c
src/matrix/sylvester.h
src/matrix/thread_matrix.c
src/matrix/thread_matrix.h
src/nnlsm
src/nnlsm/blockpivot.c
src/nnlsm/blockpivot.h
src/nnlsm/nmf_bpas
src/nnlsm/nmf_bpas/AtB.txt
src/nnlsm/nmf_bpas/PassiveSet.txt
src/nnlsm/nmf_bpas/R.txt
src/nnlsm/nmf_bpas/README.txt
src/nnlsm/nmf_bpas/U.txt
src/nnlsm/nmf_bpas/W.pdf
src/nnlsm/nmf_bpas/W.txt
src/nnlsm/nmf_bpas/example_1.m
src/nnlsm/nmf_bpas/example_2.m
src/nnlsm/nmf_bpas/nmf.m
src/nnlsm/nmf_bpas/nnlsm_activeset.m
src/nnlsm/nmf_bpas/nnlsm_blockpivot.m
src/nnlsm/nmf_bpas/plop.txt
src/nnlsm/nmf_bpas/solveNormalEqComb.m
src/nnlsm/nnlsm.c
src/nnlsm/nnlsm.h
src/nnlsm/solvenormaleqcomb.c
src/nnlsm/solvenormaleqcomb.h
src/nnlsm/sort.c
src/nnlsm/sort.h
src/pca
src/pca/calc_cov.c
src/pca/calc_cov.h
src/pca/error_pca.c
src/pca/error_pca.h
src/pca/pca.c
src/pca/pca.h
src/pca/print_pca.c
src/pca/print_pca.h
src/pca/register_pca.c
src/pca/register_pca.h
src/sNMF
src/sNMF/als.c
src/sNMF/als.h
src/sNMF/als_F.c
src/sNMF/als_F.h
src/sNMF/als_Q.c
src/sNMF/als_Q.h
src/sNMF/als_k1.c
src/sNMF/als_k1.h
src/sNMF/criteria.c
src/sNMF/criteria.h
src/sNMF/error_snmf.c
src/sNMF/error_snmf.h
src/sNMF/print_snmf.c
src/sNMF/print_snmf.h
src/sNMF/register_snmf.c
src/sNMF/register_snmf.h
src/sNMF/sNMF.c
src/sNMF/sNMF.h
src/sNMF/thread_F.c
src/sNMF/thread_F.h
src/sNMF/thread_Q.c
src/sNMF/thread_Q.h
src/sNMF/thread_snmf.c
src/sNMF/thread_snmf.h
src/stats
src/stats/beta_distribution.c
src/stats/beta_function.c
src/stats/entire_incomplete_gamma_function.c
src/stats/factorial.c
src/stats/gamma_density.c
src/stats/gamma_dist_tables.c
src/stats/gamma_distribution.c
src/stats/gamma_distribution.h
src/stats/gamma_function.c
src/stats/ln_beta_function.c
src/stats/ln_gamma_function.c
src/stats/stats.h
src/stats/student_t_distribution.c
src/stats/student_t_distribution.h
src/tracyWidom
src/tracyWidom/error_tracyWidom.c
src/tracyWidom/error_tracyWidom.h
src/tracyWidom/print_tracyWidom.c
src/tracyWidom/print_tracyWidom.h
src/tracyWidom/register_tracyWidom.c
src/tracyWidom/register_tracyWidom.h
src/tracyWidom/tracyWidom.c
src/tracyWidom/tracyWidom.h
src/tracyWidom/twtable.h
vignettes
vignettes/LEA.Rnw
vignettes/biblio.bib
vignettes/cse.bst

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.