Combine multiple TreeSummarizedExperiment objects | Subset a TSE object | Change specific trees of TSE | Session Info | Reference
Package: TreeSummarizedExperiment 2.21.0
Ruizhu Huang
TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.
Authors:
TreeSummarizedExperiment_2.21.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TreeSummarizedExperiment/json (API)
| # Install 'TreeSummarizedExperiment' in R: |
| install.packages('TreeSummarizedExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- tinyTree - A simulated phylogenetic tree with 10 tips and 9 internal nodes
On BioConductor:TreeSummarizedExperiment-2.21.0(bioc 3.24)TreeSummarizedExperiment-2.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
datarepresentationinfrastructure
Last updated from:ceaaaec489. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 203 | ||
| linux-devel-x86_64 | NOTE | 422 | ||
| source / vignettes | OK | 282 | ||
| linux-release-x86_64 | NOTE | 471 | ||
| macos-release-arm64 | NOTE | 268 | ||
| macos-oldrel-arm64 | NOTE | 268 | ||
| windows-devel | NOTE | 318 | ||
| windows-release | NOTE | 317 | ||
| windows-oldrel | NOTE | 303 | ||
| wasm-release | OK | 191 |
Exports:addLabelaggTSEaggValueasLeafasPhylocbindchangeTreecolLinkscolnames<-colTreecolTree<-colTreeNamescolTreeNames<-convertNodecountLeafcountNodedetectLoopdistNodefindAncestorfindChildfindDescendantfindOSfindSiblingisLeafjoinNodeLinkDataFramemakeTSEmatTreeprintNoderbindreferenceSeqreferenceSeq<-resolveLooprowLinksrownames<-rowTreerowTree<-rowTreeNamesrowTreeNames<-shareNodeshowNodesignalNodesubsetByLeafsubsetByNodetoTreetrackNodetransNodeTreeSummarizedExperimentunionLeafupdateObjectvertical_slot_names
Dependencies:abindapeBHBiobaseBiocGenericsBiocParallelBiostringsclicodetoolscpp11crayonDelayedArraydigestdplyrformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesglueIRangesjsonlitelambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsnlmepillarpkgconfigpurrrR6rappdirsRcpprlangS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttidytreetreeioutf8vctrswithrXVectoryulab.utils
Combine TreeSummarizedExperiment objects
Last update: 2021-01-25
Started: 2021-01-17
Introduction to TreeSummarizedExperiment
Introduction | TreeSummarizedExperiment | Anatomy of TreeSummarizedExperiment | Toy data | The construction of TreeSummarizedExperiment | The accessor functions | Assays, rowData, colData, and metadata | rowTree, colTree, rowLinks, colLinks | Reference sequence data | The subseting function | Changing the tree | Aggregation | The column dimension | The row dimension | Both dimensions | Functions operating on the phylo object. | Conversion of the node label and the node number | Find the descendants | More functions | Custom functions for the TreeSummarizedExperiment class | Session Info | Reference
Last update: 2021-01-18
Started: 2018-12-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'TreeSummarizedExperiment' package | TreeeSummarizedExperiment-package |
| add labels to nodes of a tree | addLabel |
| Perform data aggregations based on the available tree structures | aggTSE |
| Perform data aggregations based on the available tree structures | aggValue |
| change internal nodes to leaf nodes | asLeaf |
| Convert a data frame to a phylo object | asPhylo |
| Change the row or column tree | changeTree |
| count the number of leaf nodes | countLeaf |
| count the number of nodes | countNode |
| Detect loops 'detectLoop' detects loops | detectLoop |
| Calculate the distance between any two nodes on the tree | distNode |
| Find the ancestors of specified nodes | findAncestor |
| Find the children | findChild |
| Find descendants (or offsprings) | findDescendant findOS |
| find the sibling node | findSibling |
| To test whether the specified nodes are leaf nodes | isLeaf |
| LinkDataFrame: A S4 class extended from DataFrame An S4 class LinkDataFrame | LinkDataFrame-class |
| Construct a LinkDataFrame Construct a LinkDataFrame object | LinkDataFrame LinkDataFrame-constructor |
| A toy TreeSummarizedExperiment object | makeTSE |
| Transform a phylo object into a matrix. | matTree |
| To print out the node labels | printNode |
| Combine TSEs by rows or columns | cbind,TreeSummarizedExperiment-method rbind,TreeSummarizedExperiment-method TreeSummarizedExperiment-combine |
| Resolve loops 'resolveLoop' resolve loops by adding suffix to the child node. The suffix is "_i" where 'i' is a number. Please see examples. | resolveLoop |
| TreeSummarizedExperiment-accessors | colLinks colLinks,TreeSummarizedExperiment-method colnames<-,TreeSummarizedExperiment-method colTree colTree,TreeSummarizedExperiment-method colTree<- colTree<-,TreeSummarizedExperiment-method colTreeNames colTreeNames,TreeSummarizedExperiment-method colTreeNames<- colTreeNames<-,TreeSummarizedExperiment-method referenceSeq referenceSeq,TreeSummarizedExperiment-method referenceSeq<- referenceSeq<-,TreeSummarizedExperiment-method rowLinks rowLinks,TreeSummarizedExperiment-method rownames<-,TreeSummarizedExperiment-method rowTree rowTree,TreeSummarizedExperiment-method rowTree<- rowTree<-,TreeSummarizedExperiment-method rowTreeNames rowTreeNames,TreeSummarizedExperiment-method rowTreeNames<- rowTreeNames<-,TreeSummarizedExperiment-method subsetByLeaf subsetByLeaf,TreeSummarizedExperiment-method subsetByNode subsetByNode,TreeSummarizedExperiment-method TreeSummarizedExperiment-accessor [,TreeSummarizedExperiment,ANY,ANY,ANY-method [<-,TreeSummarizedExperiment,ANY,ANY,TreeSummarizedExperiment-method |
| Find the share node | shareNode |
| Find nodes on the tree | showNode |
| Join nodes | joinNode signalNode |
| A simulated phylogenetic tree with 10 tips and 9 internal nodes | tinyTree |
| Translate a data frame to a phylo object | toTree |
| track the nodes of a phylo tree | trackNode |
| Transfer between node number and node label | convertNode transNode |
| An S4 class TreeSummarizedExperiment | TreeSummarizedExperiment-class |
| Construct a TreeSummarizedExperiment object | TreeSummarizedExperiment TreeSummarizedExperiment-constructor |
| list leaf nodes that are the descendants of at least one specified node | unionLeaf |
| Update a 'TreeSummarizedExperiment' object | updateObject,TreeSummarizedExperiment-method |
