Man pages for sa-lee/starmie
Population Structure Model Inference and Visualisation
| admix | Constructor for admix object |
| admixList | Contructor for admixList |
| averagePairWiseSimilarityH | Compute average pairwise similarity between Q matrices. |
| averageQ | Convenience function for creating final Q-matrix after CLUMMP |
| bestK | Determine a suitable K value from multiple Structure runs |
| clumpak | Run the CLUMPP algorithms. |
| clumpp | Run the CLUMPP algorithms. |
| exampleAdmixture | Example admixture runs |
| exampleStructure | Example structure objects |
| fineStruct | Constructor for fineStruct object |
| getClusterAlleleFreqMat | Retrieve estimated within-cluster allele frequencies |
| getCompleteAlleleFreqMat | Retrieve estimated population allele frequencies |
| getD | Accessor methods for struct objects |
| getK | Retrieve the assumed number of populations from 'struct' or... |
| getQ | Retrieve Q matrix from 'struct' or 'admix' objects. |
| getStephens | Use the Stephen's method to permute sample labels |
| loadAdmixture | Read Admixture Output |
| loadFineStructure | Read fineSTRUCTURE Output |
| loadStructure | Read Structure Output |
| plotBar | Generate a barplot of a Structure or Admixture run. |
| plotFineStructDendro | Plot dendrogram from output of fineStructure |
| plotMCMC | Plot STRUCTURE MCMC chains |
| plotMDS | Plot principal coordinates from Q-matrix, struct or admix... |
| plotMultiK | Generate a barplot for multiple values of K.. |
| plotPWCoancestry | fineSTRUCTURE pairwise coancestry plot |
| plotPWCoincidence | fineSTRUCTURE pairwise coincidence plot |
| plotTreeBar | Generate a barplot of a Structure or Admixture run. |
| runStructure | Run STRUCTURE in current path |
| simulateQ | Simulate random Q-matrix and permutations with replications |
| struct | Constructor for struct object |
| structList | Constructor for a structList object |
