LEA: an R package for Landscape and Ecological Association Studies

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Documentation for package ‘LEA’ version 3.19.8

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A B C E G I L M O P Q R S T V W Z misc

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

-- A --

adjusted.pvalues-method Fitting Latent Factor Mixed Models (MCMC algorithm)
ancestrymap 'ancestrymap' format description
ancestrymap2geno Convert from 'ancestrymap' to 'geno' format
ancestrymap2lfmm Convert from 'ancestrymap' to 'lfmm' format

-- B --

barchart Bar plot representation of an snmf Q-matrix
barchart-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- C --

combine.lfmmProject Fitting Latent Factor Mixed Models (MCMC algorithm)
combine.lfmmProject-method Fitting Latent Factor Mixed Models (MCMC algorithm)
combine.snmfProject Estimates individual ancestry coefficients and ancestral allele frequencies.
combine.snmfProject-method Estimates individual ancestry coefficients and ancestral allele frequencies.
create.dataset create a data set with masked data
cross.entropy Cross-entropy criterion for snmf runs
cross.entropy-method Estimates individual ancestry coefficients and ancestral allele frequencies.
cross.entropy.estimation compute the cross-entropy criterion

-- E --

eigenvalues Principal Component Analysis
eigenvalues-method Principal Component Analysis
eigenvectors Principal Component Analysis
eigenvectors-method Principal Component Analysis
env Environmental input file format for 'lfmm'
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
export.lfmmProject Fitting Latent Factor Mixed Models (MCMC algorithm)
export.lfmmProject-method Fitting Latent Factor Mixed Models (MCMC algorithm)
export.pcaProject Principal Component Analysis
export.pcaProject-method Principal Component Analysis
export.snmfProject Estimates individual ancestry coefficients and ancestral allele frequencies.
export.snmfProject-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- G --

G Ancestral allele frequencies from a snmf run
G-method Estimates individual ancestry coefficients and ancestral allele frequencies.
genetic.gap Genetic gap: genetic offset and genetic distance between environments.
genetic.offset Genetic offset and genetic distance between environments.
geno Input file for 'snmf'
geno2lfmm Convert from 'geno' to 'lfmm' format

-- I --

import.lfmmProject Fitting Latent Factor Mixed Models (MCMC algorithm)
import.lfmmProject-method Fitting Latent Factor Mixed Models (MCMC algorithm)
import.pcaProject Principal Component Analysis
import.pcaProject-method Principal Component Analysis
import.snmfProject Estimates individual ancestry coefficients and ancestral allele frequencies.
import.snmfProject-method Estimates individual ancestry coefficients and ancestral allele frequencies.
impute Impute missing genotypes using an snmf object
impute-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- L --

lfmm Fitting Latent Factor Mixed Models (MCMC algorithm)
lfmm.data Input file for 'lfmm'
lfmm.pvalues P-values from lfmm runs
lfmm.pvalues-method Fitting Latent Factor Mixed Models (MCMC algorithm)
lfmm2 Fitting Latent Factor Mixed Models (Least squares algorithm)
lfmm2.test P-values adjusted for latent factors computed by 'lfmm2'.
lfmm2.test-method Fitting Latent Factor Mixed Models (Least squares algorithm)
lfmm2geno Convert from 'lfmm' to 'geno' format
lfmmClass-method z-scores from an lfmm run
load.lfmmProject Fitting Latent Factor Mixed Models (MCMC algorithm)
load.lfmmProject-method Fitting Latent Factor Mixed Models (MCMC algorithm)
load.pcaProject Principal Component Analysis
load.pcaProject-method Principal Component Analysis
load.snmfProject Estimates individual ancestry coefficients and ancestral allele frequencies.
load.snmfProject-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- M --

mlog10p.values-method Fitting Latent Factor Mixed Models (MCMC algorithm)

-- O --

offset_example Example data for genetic offset analysis

-- P --

p.values-method Fitting Latent Factor Mixed Models (MCMC algorithm)
pca Principal Component Analysis
ped 'ped' format description
ped2geno Convert from 'ped' to 'geno' format
ped2lfmm Convert from 'ped' to 'lfmm' format
plot-method Fitting Latent Factor Mixed Models (MCMC algorithm)
plot-method Principal Component Analysis
plot-method Estimates individual ancestry coefficients and ancestral allele frequencies.
projections Principal Component Analysis
projections-method Principal Component Analysis

-- Q --

Q Admixture coefficients from a snmf run
Q-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- R --

read.env Read environmental file in the 'env'format
read.geno read a file in the 'geno' format
read.lfmm Read files in the 'lfmm' format
read.zscore Read the output files of 'lfmm'
remove.lfmmProject Fitting Latent Factor Mixed Models (MCMC algorithm)
remove.lfmmProject-method Fitting Latent Factor Mixed Models (MCMC algorithm)
remove.pcaProject Principal Component Analysis
remove.pcaProject-method Principal Component Analysis
remove.snmfProject Estimates individual ancestry coefficients and ancestral allele frequencies.
remove.snmfProject-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- S --

sdev Principal Component Analysis
sdev-method Principal Component Analysis
show-method Fitting Latent Factor Mixed Models (MCMC algorithm)
show-method Principal Component Analysis
show-method Estimates individual ancestry coefficients and ancestral allele frequencies.
snmf Estimates individual ancestry coefficients and ancestral allele frequencies.
snmf.pvalues P-values for snmf population differentiation tests
snmf.pvalues-method Estimates individual ancestry coefficients and ancestral allele frequencies.
struct2geno Conversion from the STRUCTURE format to the geno format.
summary-method Fitting Latent Factor Mixed Models (MCMC algorithm)
summary-method Principal Component Analysis
summary-method Estimates individual ancestry coefficients and ancestral allele frequencies.

-- T --

tracy.widom Tracy-Widom test for eigenvalues
tracy.widom-method Principal Component Analysis
tutorial Example tutorial data sets

-- V --

vcf 'vcf' format description
vcf2geno Convert from 'vcf' to 'geno' format
vcf2lfmm Convert from 'vcf' to 'lfmm' format

-- W --

write.env Write files in the 'env' format
write.geno Write files in the 'geno' format
write.lfmm Write files in the 'lfmm' format

-- Z --

z.scores z-scores from an lfmm run
z.scores-method Fitting Latent Factor Mixed Models (MCMC algorithm)
zscore.format Output file format for 'lfmm'

-- misc --

$-method Principal Component Analysis