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

ancestrymap'ancestrymap' format description
ancestrymap2genoConvert from 'ancestrymap' to 'geno' format
ancestrymap2lfmmConvert from 'ancestrymap' to 'lfmm' format
barchartBar plot representation of an snmf Q-matrix
crossEntropyCross-entropy criterion for snmf runs
envEnvironmental input file format for 'lfmm'
GAncestral allele frequencies from a snmf run
genetic_offsetPopulation genetic offset under new environments.
genoInput file for 'snmf'
geno2lfmmConvert from 'geno' to 'lfmm' format
imputeImpute missing genotypes using an snmf object
lfmmInput file for 'lfmm'
lfmm2Fitting Latent Factor Mixed Models (Least squares algorithm)
lfmm2genoConvert from 'lfmm' to 'geno' format
lfmm2_testP-values adjusted for latent factors computed by 'lfmm2'.
lfmm_pvaluesP-values from lfmm runs
main_createDataSetcreate a data set with masked data
main_crossEntropyEstimationcompute the cross-entropy criterion
main_LFMMFitting Latent Factor Mixed Models (MCMC algorithm)
main_pcaPrincipal Component Analysis
main_sNMFEstimates individual ancestry coefficients and ancestral...
main_tracyWidomTracy-Widom test for eigenvalues
ped'ped' format description
ped2genoConvert from 'ped' to 'geno' format
ped2lfmmConvert from 'ped' to 'lfmm' format
QAdmixture coefficients from a snmf run
readEnvRead environmental file in the 'env'format
readGenoread a file in the 'geno' format
readLfmmRead files in the 'lfmm' format
readZscoreRead the output files of 'lfmm'
Replop-packageLEA: an R package for Landscape and Ecological Associations...
snmf_pvaluesP-values for snmf population differentiation tests
struct2genoConversion from the STRUCTURE format to the geno format.
tutorialExample tutorial data sets
vcf'vcf' format description
vcf2genoConvert from 'vcf' to 'geno' format
vcf2lfmmConvert from 'vcf' to 'lfmm' format
writeEnvWrite files in the 'env' format
writeGenoWrite files in the 'geno' format
writeLFMMWrite files in the 'lfmm' format
zscoreOutput file format for 'lfmm'
zscoresz-scores from a lfmm run
LEA documentation built on Nov. 8, 2020, 8:19 p.m.