Man pages for sa-lee/starmie
Population Structure Model Inference and Visualisation

admixConstructor for admix object
admixListContructor for admixList
averagePairWiseSimilarityHCompute average pairwise similarity between Q matrices.
averageQConvenience function for creating final Q-matrix after CLUMMP
bestKDetermine a suitable K value from multiple Structure runs
clumpakRun the CLUMPP algorithms.
clumppRun the CLUMPP algorithms.
exampleAdmixtureExample admixture runs
exampleStructureExample structure objects
fineStructConstructor for fineStruct object
getClusterAlleleFreqMatRetrieve estimated within-cluster allele frequencies
getCompleteAlleleFreqMatRetrieve estimated population allele frequencies
getDAccessor methods for struct objects
getKRetrieve the assumed number of populations from 'struct' or...
getQRetrieve Q matrix from 'struct' or 'admix' objects.
getStephensUse the Stephen's method to permute sample labels
loadAdmixtureRead Admixture Output
loadFineStructureRead fineSTRUCTURE Output
loadStructureRead Structure Output
plotBarGenerate a barplot of a Structure or Admixture run.
plotFineStructDendroPlot dendrogram from output of fineStructure
plotMDSPlot principal coordinates from Q-matrix, struct or admix...
plotMultiKGenerate a barplot for multiple values of K..
plotPWCoancestryfineSTRUCTURE pairwise coancestry plot
plotPWCoincidencefineSTRUCTURE pairwise coincidence plot
plotTreeBarGenerate a barplot of a Structure or Admixture run.
runStructureRun STRUCTURE in current path
simulateQSimulate random Q-matrix and permutations with replications
structConstructor for struct object
structListConstructor for a structList object
sa-lee/starmie documentation built on May 25, 2017, 10:21 p.m.