Man pages for fionarhuang/TreeSummarizedExperiment
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
| addLabel | add labels to nodes of a tree |
| aggTSE | Perform data aggregations based on the available tree... |
| aggValue | Perform data aggregations based on the available tree... |
| asLeaf | change internal nodes to leaf nodes |
| asPhylo | Convert a data frame to a phylo object |
| changeTree | Change the row or column tree |
| convertNode | Transfer between node number and node label |
| countLeaf | count the number of leaf nodes |
| countNode | count the number of nodes |
| detectLoop | Detect loops 'detectLoop' detects loops |
| distNode | Calculate the distance between any two nodes on the tree |
| dot-all_equal_in_list | test all elements in a list are equal |
| dot-all_have_DNAStringSet | test all TSEs have DNAStringSet in the referenceSeq slot |
| dot-all_have_DNAStringSetList | test all TSEs have DNAStringSetList in the referenceSeq slot |
| dot-all_nonnull_in_list | all elements in the list are NULL |
| dot-all_null_in_list | all elements in the list are NULL |
| dot-any_null_in_list | Any element in the list is NULL |
| dot-auto_rename_list | rename a list automatically to avoid duplicated names |
| dot-bind_link_tree | bind links & trees when combine TSE |
| dot-is_equal_link | The links & trees in the specified dim are consistent |
| dot-match_phylo | match a phylo to a list of phylo |
| dot-match_phylo_list | match a list of phylo (x.phys) against to a list of phylo... |
| dot-match_x_dupY | convert char. indicator to num. indicator |
| dot-name_y_with_x | name y with x |
| dot-numeric_ij | convert char. indicator to num. indicator |
| dot-rbind_refSeq | rbind referenceSeq |
| dot-replace_link_tree_1d | replace row/col links & trees |
| dot-subset_leaf | update dimLinks and dimTree (used in subsetByLeaf) |
| dot-update_whichTree | update the 'whichTree' column in row/column link data |
| findAncestor | Find the ancestors of specified nodes |
| findChild | Find the children |
| findDescendant | Find descendants (or offsprings) |
| findSibling | find the sibling node |
| isLeaf | To test whether the specified nodes are leaf nodes |
| joinNode | Join nodes |
| LinkDataFrame-class | LinkDataFrame: A S4 class extended from DataFrame An S4 class... |
| LinkDataFrame-constructor | Construct a LinkDataFrame Construct a LinkDataFrame object |
| makeTSE | A toy TreeSummarizedExperiment object |
| matTree | Transform a phylo object into a matrix. |
| phylo | phylo: A S3 class for the phylogenetic tree |
| printNode | To print out the node labels |
| resolveLoop | Resolve loops 'resolveLoop' resolve loops by adding suffix to... |
| shareNode | Find the share node |
| showNode | Find nodes on the tree |
| tinyTree | A simulated phylogenetic tree with 10 tips and 9 internal... |
| toTree | Translate a data frame to a phylo object |
| trackNode | track the nodes of a phylo tree |
| TreeeSummarizedExperiment-package | The 'TreeSummarizedExperiment' package |
| TreeSummarizedExperiment-accessor | TreeSummarizedExperiment-accessors |
| TreeSummarizedExperiment-class | An S4 class TreeSummarizedExperiment |
| TreeSummarizedExperiment-combine | Combine TSEs by rows or columns |
| TreeSummarizedExperiment-constructor | Construct a TreeSummarizedExperiment object |
| TreeSummarizedExperiment-internal | TreeSummarizedExperiment internals |
| unionLeaf | list leaf nodes that are the descendants of at least one... |
| updateObject-TreeSummarizedExperiment-method | Update a 'TreeSummarizedExperiment' object |
