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. |
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 |
barchart | Bar plot representation of an snmf Q-matrix |
barchart-method | Estimates individual ancestry coefficients and ancestral allele frequencies. |
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 |
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 | 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 |
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. |
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. |
mlog10p.values-method | Fitting Latent Factor Mixed Models (MCMC algorithm) |
offset_example | Example data for genetic offset analysis |
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 | 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 (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. |
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. |
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 an lfmm run |
z.scores-method | Fitting Latent Factor Mixed Models (MCMC algorithm) |
zscore.format | Output file format for 'lfmm' |
$-method | Principal Component Analysis |