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 |