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.

AuthorEric Frichot <eric.frichot@gmail.com>, Olivier Francois <olivier.francois@imag.fr>
Date of publicationNone
MaintainerEric Frichot <eric.frichot@gmail.com>
LicenseGPL-3
Version1.6.0
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

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

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