Man pages for markrobinsonuzh/treeAGG
Tree Aggregation
| bigTree | A simulated phylogenetic tree with 800 tips and 799 internal... |
| checkLSE | valid leafSummarizedExperiment class |
| dot-addBranch | Color a branch |
| dot-addLegend | Add legend '.addLegend' customizes the legend. |
| dot-addPoint | Add points to the tree plot |
| dot-addZoom | Visualize the phylogenetic tree |
| dot-colScale | Customize the color |
| dot-designMatrix | Create design matrix |
| dot-doCount | generate a count table |
| dot-doData | Simulate a count table |
| dot-doFC | Generate the fold change |
| dot-fdr0 | Calculate false discoveries and discoveries |
| dot-findParallel | find parallel nodes |
| dot-infLoc | Provide the information of two branches |
| dot-pickLoc | Select branches |
| dot-sizeScale | Customize the scale |
| dot-tpr0 | Calculate true positives and positives |
| exTree | A simulated phylogenetic tree with 50 tips and 49 internal... |
| fdr | Calculate false discovery rate (fdr) on a tree structure |
| findAncestor | Find the ancestors of specified nodes |
| findOS | Find descendants (or offsprings) |
| findSibling | find the sibling node |
| internal_rowData-class | internal_rowData: A virtual class —————— A... |
| isLeaf | To test whether the specified nodes are leaf nodes |
| leafSummarizedExperiment-class | An S4 class leafSummarizedExperiment |
| leafSummarizedExperiment-constructor | Construct a leafSummarizedExperiment object |
| matTree | Transform a phylo object into a matrix. |
| nodeValue | Calculate entity values at internal nodes |
| parEstimate | Parameter estimation in Dirichlet-multinomial distribution |
| phylo | phylo: A S3 class for the phylogenetic tree |
| rmDesc | Remove nodes which are the descendants of other nodes |
| runEdgeR | Test for differential abundance: method 'treeAGG-DA-edgeR' |
| selNode | Select branches |
| shareNode | Find the share node |
| signalNode | find the optimal nodes to short result. |
| simData | Simulate different scenarios of abundance change in entities |
| tinyTree | A simulated phylogenetic tree with 10 tips and 9 internal... |
| topNodes | Table of the top differential nodes |
| tpr | Calculate true positive rate (TPR) on a tree structure |
| transNode | Transfer between node number and node label |
| treeAGG | Tree aggregation |
| treePlot | Visualize the phylogenetic tree |
| treeSummarizedExperiment-accessor | Accessor functions for treeSummarizedExperiment |
| treeSummarizedExperiment-class | An S4 class treeSummarizedExperiment |
| treeSummarizedExperiment-constructor | Construct a treeSummarizedExperiment object |
| updateTSE | update the treeSummarizedExperiment object |
| viewSim | visualize simulated scenario |
