LEA: an R package for Landscape and Ecological Association Studies


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Documentation for package ‘LEA’ version 2.8.0

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A B C E G I L M 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
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
combine.lfmmProject-method Fitting Latent Factor Mixed Models
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
export.lfmmProject-method Fitting Latent Factor Mixed Models
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.
geno Input file for 'snmf'
geno2lfmm Convert from 'geno' to 'lfmm' format

-- I --

import.lfmmProject Fitting Latent Factor Mixed Models
import.lfmmProject-method Fitting Latent Factor Mixed Models
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
lfmm.data Input file for 'lfmm'
lfmm.pvalues P-values from lfmm runs
lfmm.pvalues-method Fitting Latent Factor Mixed Models
lfmm2geno Convert from 'lfmm' to 'geno' format
load.lfmmProject Fitting Latent Factor Mixed Models
load.lfmmProject-method Fitting Latent Factor Mixed Models
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

-- P --

p.values-method Fitting Latent Factor Mixed Models
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
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
remove.lfmmProject-method Fitting Latent Factor Mixed Models
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
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
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 a lfmm run
z.scores-method Fitting Latent Factor Mixed Models
zscore.format Output file format for 'lfmm'

-- misc --

$-method Principal Component Analysis