Package: LEA 3.19.1
Olivier Francois
LEA: LEA: an R package for Landscape and Ecological Association Studies
LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.
Authors:
LEA_3.19.1.tar.gz
LEA_3.19.1.zip(r-4.5)LEA_3.19.1.zip(r-4.4)LEA_3.19.1.zip(r-4.3)
LEA_3.19.1.tgz(r-4.4-x86_64)LEA_3.19.1.tgz(r-4.4-arm64)LEA_3.19.1.tgz(r-4.3-x86_64)LEA_3.19.1.tgz(r-4.3-arm64)
LEA_3.19.1.tar.gz(r-4.5-noble)LEA_3.19.1.tar.gz(r-4.4-noble)
LEA.pdf |LEA.html✨
LEA/json (API)
NEWS
| # Install 'LEA' in R: |
| install.packages('LEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- example_ancestrymap - 'ancestrymap' format description
- example_geno - Input file for 'snmf'
- example_lfmm - Input file for 'lfmm'
- example_ped - 'ped' format description
- example_vcf - 'vcf' format description
- offset_example - Example data for genetic offset analysis
On BioConductor:LEA-3.19.1(bioc 3.21)LEA-3.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarestatistical methodclusteringregressionopenblas
Last updated 1 months agofrom:a37ac6c3b2. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 09 2024 |
| R-4.5-win-x86_64 | OK | Nov 09 2024 |
| R-4.5-linux-x86_64 | OK | Nov 09 2024 |
| R-4.4-win-x86_64 | OK | Dec 09 2024 |
| R-4.4-mac-x86_64 | OK | Dec 09 2024 |
| R-4.4-mac-aarch64 | OK | Dec 09 2024 |
| R-4.3-win-x86_64 | OK | Dec 09 2024 |
| R-4.3-mac-x86_64 | OK | Dec 09 2024 |
| R-4.3-mac-aarch64 | OK | Dec 09 2024 |
Exports:ancestrymap2genoancestrymap2lfmmbarchartcombine.lfmmProjectcombine.snmfProjectcreate.datasetcross.entropycross.entropy.estimationexport.lfmmProjectexport.pcaProjectexport.snmfProjectGgenetic.gapgenetic.offsetgeno2lfmmimport.lfmmProjectimport.pcaProjectimport.snmfProjectimputelfmmlfmm.pvalueslfmm2lfmm2.testlfmm2genoload.lfmmProjectload.pcaProjectload.snmfProjectpcaped2genoped2lfmmplotQread.envread.genoread.lfmmread.zscoreremove.lfmmProjectremove.pcaProjectremove.snmfProjectshowsnmfsnmf.pvaluesstruct2genosummarytracy.widomvcf2genovcf2lfmmwrite.envwrite.genowrite.lfmmz.scores
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| LEA: an R package for Landscape and Ecological Associations studies. | LEA-package |
| 'ancestrymap' format description | ancestrymap example_ancestrymap |
| Convert from 'ancestrymap' to 'geno' format | ancestrymap2geno |
| Convert from 'ancestrymap' to 'lfmm' format | ancestrymap2lfmm |
| Bar plot representation of an snmf Q-matrix | barchart |
| create a data set with masked data | create.dataset |
| Cross-entropy criterion for snmf runs | cross.entropy |
| compute the cross-entropy criterion | cross.entropy.estimation |
| Environmental input file format for 'lfmm' | env |
| Ancestral allele frequencies from a snmf run | G |
| Genetic gap: genetic offset and genetic distance between environments. | genetic.gap |
| Genetic offset and genetic distance between environments. | genetic.offset |
| Input file for 'snmf' | example_geno geno |
| Convert from 'geno' to 'lfmm' format | geno2lfmm |
| Impute missing genotypes using an snmf object | impute |
| Fitting Latent Factor Mixed Models (MCMC algorithm) | adjusted.pvalues,lfmmProject-method combine.lfmmProject combine.lfmmProject,character,character-method export.lfmmProject export.lfmmProject,character-method import.lfmmProject import.lfmmProject,character-method lfmm lfmm.pvalues,lfmmProject-method load.lfmmProject load.lfmmProject,character-method mlog10p.values,lfmmProject-method p.values,lfmmProject-method plot,lfmmProject-method remove.lfmmProject remove.lfmmProject,character-method show,lfmmClass-method show,lfmmProject-method summary,lfmmProject-method z.scores,lfmmProject-method |
| Input file for 'lfmm' | example_lfmm lfmm.data |
| P-values from lfmm runs | lfmm.pvalues |
| Fitting Latent Factor Mixed Models (Least squares algorithm) | lfmm2 lfmm2.test,lfmm2Class-method |
| P-values adjusted for latent factors computed by 'lfmm2'. | lfmm2.test |
| Convert from 'lfmm' to 'geno' format | lfmm2geno |
| Example data for genetic offset analysis | offset_example |
| Principal Component Analysis | $,pcaProject-method eigenvalues eigenvalues,pcaProject-method eigenvectors eigenvectors,pcaProject-method export.pcaProject export.pcaProject,character-method import.pcaProject import.pcaProject,character-method load.pcaProject load.pcaProject,character-method pca plot,pcaProject-method projections projections,pcaProject-method remove.pcaProject remove.pcaProject,character-method sdev sdev,pcaProject-method show,pcaProject-method summary,pcaProject-method tracy.widom,pcaProject-method |
| 'ped' format description | example_ped ped |
| Convert from 'ped' to 'geno' format | ped2geno |
| Convert from 'ped' to 'lfmm' format | ped2lfmm |
| Admixture coefficients from a snmf run | Q |
| Read environmental file in the 'env'format | read.env |
| read a file in the 'geno' format | read.geno |
| Read files in the 'lfmm' format | read.lfmm |
| Read the output files of 'lfmm' | read.zscore |
| Estimates individual ancestry coefficients and ancestral allele frequencies. | barchart,snmfProject-method combine.snmfProject combine.snmfProject,character,character-method cross.entropy,snmfProject-method export.snmfProject export.snmfProject,character-method G,snmfProject-method import.snmfProject import.snmfProject,character-method impute,snmfProject-method load.snmfProject load.snmfProject,character-method plot,snmfProject-method Q,snmfProject-method remove.snmfProject remove.snmfProject,character-method show,snmfClass-method show,snmfProject-method snmf snmf.pvalues,snmfProject-method summary,snmfProject-method |
| P-values for snmf population differentiation tests | snmf.pvalues |
| Conversion from the STRUCTURE format to the geno format. | struct2geno |
| Tracy-Widom test for eigenvalues | tracy.widom |
| Example tutorial data sets | tutorial |
| 'vcf' format description | example_vcf vcf |
| Convert from 'vcf' to 'geno' format | vcf2geno |
| Convert from 'vcf' to 'lfmm' format | vcf2lfmm |
| Write files in the 'env' format | write.env |
| Write files in the 'geno' format | write.geno |
| Write files in the 'lfmm' format | write.lfmm |
| z-scores from an lfmm run | lfmmClass-method z.scores |
| Output file format for 'lfmm' | zscore.format |