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

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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.

Author
Eric Frichot <eric.frichot@gmail.com>, Olivier Francois <olivier.francois@imag.fr>
Date of publication
None
Maintainer
Eric Frichot <eric.frichot@gmail.com>
License
GPL-3
Version
1.6.0
URLs

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

Files in this package

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