LEA-package | LEA: an R package for Landscape and Ecological Associations studies. |
$-method | Principal Component Analysis |
ancestrymap | 'ancestrymap' format description |
ancestrymap2geno | Convert from 'ancestrymap' to 'geno' format |
ancestrymap2lfmm | Convert from 'ancestrymap' to 'lfmm' format |
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 |
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 |
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' |