Man pages for bcm-uga/TESS3_encho_sen
Inference of Spatial Population Genetic Structure
| as.qmatrix | Converts into Q matrix |
| barplot.tess3Q | Barplot representation of a Q-matrix |
| CalculateEmpiricalGenSemivariogram | Calculate empirical semi variance from genotype matrix. |
| CalculateEmpiricalSemivariogram | Calculate empirical semi-variance. |
| CheckCoord | Raise error if coord is not well formated. |
| CheckW | Raise error if W is not well formated. |
| CheckWCoord | Raise error if W and coord are not consistent. |
| CheckX | Raise error if X is not well formated. |
| CheckXBin | Raise error if XBin is not well formated. |
| CheckXBinCoord | Raise error if XBin and coord are not consistent. |
| CheckXBinW | Raise error if XBin and W are not consistent. |
| CheckXCoord | Raise error if X and coord are not consistent. |
| CheckXW | Raise error if X and W are not consistent. |
| ComputeAveragedCrossEntropy | Compute average cross entropy |
| ComputeChi2AndPvalue | Convert Fst into chi2 and compute p value |
| ComputeEigenValuesWithIgraphArpack | Compute eigen values with IgraphArpack. |
| ComputeEigenValuesWithRSpectra | Compute eigen values with RSpectra. |
| ComputeExponetialWeight | Compute graph matrix with an exponiential function. |
| ComputeFst | Compute Fst statistic |
| ComputeGraphLaplacian | Compute laplacian of a graph. |
| ComputeHeatKernelWeight | Compute graph matrix with the heat kernel function. |
| ComputeHeatKernelWeightSparse | Compute graph sparse matrix with the heat kernel function. |
| ComputeMeanDist | Compute the average distance between points. |
| ComputeRmse | Compute root squared mean error |
| ComputeRmseWithBestPermutation | Compute the root mean square error between matrix by... |
| ComputeRmseWithBestPermutationGreedy | Compute the root mean square error between matrix by... |
| ComputeSpatialPenalty | Compute the value spatial penalty used in TESS3 objectif... |
| ComputeTscoreAndPvalue | Convert Fst into t-score and compute p value |
| ComputeWindow | Compute the graph window. |
| CreatePalette | Create a list of palettes |
| data.at | TODOC |
| data.for.test | TODOC |
| DebugMessage | Print a message if getOption("tess3r.debug") is not null |
| durand09 | TODOC |
| FieldsKrigModel | Return an interpolation function. Return a wrapper function... |
| FieldsTpsModel | Return an interpolation function. Return a wrapper function... |
| Gettess3res | Get tess3 run result |
| ggtess3Q | Display geographic maps of ancestry coefficients using the... |
| GtoFreq | Compute allele frequency matrix from genotype frequency... |
| ImputeRandom | Impute missing values |
| is.tess3 | Test if x is a tess3project object |
| is.tess3Main | Title |
| PlotInterpotationAll | Plot all the interpolation surfaces on several graphs. |
| PlotInterpotationMax | Plot map with the maximum values of the interpolation... |
| PlotPiechartAncestryCoef | Plot pie chart of ancestry coefficient. |
| plot.tess3 | Plot cross-validation errors for all values of number of... |
| plot.tess3Main | Title |
| plot.tess3pvalue | Manhattan plot for tess3 significance values. |
| plot.tess3Q | Display geographic maps of ancestry coefficients |
| pvalue | Get p-values from a genome scan for selection |
| qmatrix | Get Q matrix estimate |
| rmse.tess3Main | Title |
| run.ms | Helper function which call ms. |
| SampleDistFromCenterDirichletQ | For population the center mu_k is computed. Then D_i_k =... |
| SampleDistFromCenterQ | For population the center mu_k is computed. Then D_i_k =... |
| SampleFuncQ | Sample ancestral coefficient matrix such as Q = f(coord). |
| SampleGenoFromGenerativeModelTESS3 | Sample genotype from the TESS3 generative model. |
| SampleGenoOFWithMs | Sample ancestral population with ms 2 island model. Then... |
| SampleNormalClusterCoord | sample coord such as a mixture of K cluster distributed with... |
| SampleTESS2.3Q | sample Q as describe in "Spatial Inference of Admixture... |
| SampleUnifDirichletG | sample G such as G_dl+._k ~ Dirichlet(1/(ploidy + 1)) |
| SampleUnifQ | Sample ancestral coefficient matrix such as alpha ~ unif(0,1)... |
| summary.tess3 | Title |
| summary.tess3Main | Summary of tess3 object. |
| tess2tess3 | Import input files from the STRUCTURE and TESS formats |
| tess3 | Estimate ancestry coefficients and run genome scans for... |
| tess3Main | Estimate ancestry coefficients and run genome scans for... |
| tess3r | tess3r : estimation of spatial population structure |
| TestRequiredPkg | Test if a package is installed. |
| X2XBin | Binary coding of the genotype data matrix. |
| XBin2X | Convert the binary genotype matrix into genotype matrix. |
