LEA: an R package for Landscape and Ecological Association Studies


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Documentation for package ‘LEA’ version 1.6.0

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LEA-package LEA: an R package for Landscape and Ecological Associations studies.
$-method Principal Component Analysis
adjusted.pvalues adjusted p-values from a lfmm run
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
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 from snmf runs
cross.entropy-method Estimates individual ancestry coefficients and ancestral allele frequencies.
cross.entropy.estimation compute the cross-entropy criterion
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 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
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.
lfmm Fitting Latent Factor Mixed Models
lfmm.data Input file for 'lfmm'
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.
mlog10p.values -log10(p-values) from a lfmm run
mlog10p.values-method Fitting Latent Factor Mixed Models
p.values p-values from a lfmm run
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 Admixture coefficients from a snmf run
Q-method Estimates individual ancestry coefficients and ancestral allele frequencies.
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.
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.
summary-method Fitting Latent Factor Mixed Models
summary-method Principal Component Analysis
summary-method Estimates individual ancestry coefficients and ancestral allele frequencies.
tracy.widom Tracy-Widom test for eigenvalues
tracy.widom-method Principal Component Analysis
tutorial Example tutorial data sets
vcf 'vcf' format description
vcf2geno Convert from 'vcf' to 'geno' format
vcf2lfmm Convert from 'vcf' to 'lfmm' format
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.scores z-scores from a lfmm run
z.scores-method Fitting Latent Factor Mixed Models
zscore.format Output file format for 'lfmm'