Man pages for cayek/TESS3_encho_sen
Inference of Spatial Population Genetic Structure

as.qmatrixConverts into Q matrix
barplot.tess3QBarplot representation of a Q-matrix
CalculateEmpiricalGenSemivariogramCalculate empirical semi variance from genotype matrix.
CalculateEmpiricalSemivariogramCalculate empirical semi-variance.
CheckCoordRaise error if coord is not well formated.
CheckWRaise error if W is not well formated.
CheckWCoordRaise error if W and coord are not consistent.
CheckXRaise error if X is not well formated.
CheckXBinRaise error if XBin is not well formated.
CheckXBinCoordRaise error if XBin and coord are not consistent.
CheckXBinWRaise error if XBin and W are not consistent.
CheckXCoordRaise error if X and coord are not consistent.
CheckXWRaise error if X and W are not consistent.
ComputeAveragedCrossEntropyCompute average cross entropy
ComputeChi2AndPvalueConvert Fst into chi2 and compute p value
ComputeEigenValuesWithIgraphArpackCompute eigen values with IgraphArpack.
ComputeEigenValuesWithRSpectraCompute eigen values with RSpectra.
ComputeExponetialWeightCompute graph matrix with an exponiential function.
ComputeFstCompute Fst statistic
ComputeGraphLaplacianCompute laplacian of a graph.
ComputeHeatKernelWeightCompute graph matrix with the heat kernel function.
ComputeHeatKernelWeightSparseCompute graph sparse matrix with the heat kernel function.
ComputeMeanDistCompute the average distance between points.
ComputeRmseCompute root squared mean error
ComputeRmseWithBestPermutationCompute the root mean square error between matrix by...
ComputeRmseWithBestPermutationGreedyCompute the root mean square error between matrix by...
ComputeSpatialPenaltyCompute the value spatial penalty used in TESS3 objectif...
ComputeTscoreAndPvalueConvert Fst into t-score and compute p value
ComputeWindowCompute the graph window.
CreatePaletteCreate a list of palettes
data.atTODOC
data.for.testTODOC
DebugMessagePrint a message if getOption("tess3r.debug") is not null
durand09TODOC
FieldsKrigModelReturn an interpolation function. Return a wrapper function...
FieldsTpsModelReturn an interpolation function. Return a wrapper function...
Gettess3resGet tess3 run result
ggtess3QDisplay geographic maps of ancestry coefficients using the...
GtoFreqCompute allele frequency matrix from genotype frequency...
ImputeRandomImpute missing values
is.tess3Test if x is a tess3project object
is.tess3MainTitle
PlotInterpotationAllPlot all the interpolation surfaces on several graphs.
PlotInterpotationMaxPlot map with the maximum values of the interpolation...
PlotPiechartAncestryCoefPlot pie chart of ancestry coefficient.
plot.tess3Plot cross-validation errors for all values of number of...
plot.tess3MainTitle
plot.tess3pvalueManhattan plot for tess3 significance values.
plot.tess3QDisplay geographic maps of ancestry coefficients
pvalueGet p-values from a genome scan for selection
qmatrixGet Q matrix estimate
rmse.tess3MainTitle
run.msHelper function which call ms.
SampleDistFromCenterDirichletQFor population the center mu_k is computed. Then D_i_k =...
SampleDistFromCenterQFor population the center mu_k is computed. Then D_i_k =...
SampleFuncQSample ancestral coefficient matrix such as Q = f(coord).
SampleGenoFromGenerativeModelTESS3Sample genotype from the TESS3 generative model.
SampleGenoOFWithMsSample ancestral population with ms 2 island model. Then...
SampleNormalClusterCoordsample coord such as a mixture of K cluster distributed with...
SampleTESS2.3Qsample Q as describe in "Spatial Inference of Admixture...
SampleUnifDirichletGsample G such as G_dl+._k ~ Dirichlet(1/(ploidy + 1))
SampleUnifQSample ancestral coefficient matrix such as alpha ~ unif(0,1)...
summary.tess3Title
summary.tess3MainSummary of tess3 object.
tess2tess3Import input files from the STRUCTURE and TESS formats
tess3Estimate ancestry coefficients and run genome scans for...
tess3MainEstimate ancestry coefficients and run genome scans for...
tess3rtess3r : estimation of spatial population structure
TestRequiredPkgTest if a package is installed.
X2XBinBinary coding of the genotype data matrix.
XBin2XConvert the binary genotype matrix into genotype matrix.
cayek/TESS3_encho_sen documentation built on July 3, 2017, 4:26 p.m.