Package: TreeSummarizedExperiment 2.13.0

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:Ruizhu Huang [aut, cre], Felix G.M. Ernst [ctb]

# 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-2.13.0(bioc 3.20)TreeSummarizedExperiment-2.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

datarepresentation infrastructure

51 exports 7.80 score 67 dependencies 16 dependents 1 mentions 235 scripts 2.8k downloads

Last updated 5 months agofrom:b6da78c634. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 28 2024
R-4.5-win	NOTE	Sep 28 2024
R-4.5-linux	NOTE	Sep 28 2024
R-4.4-win	NOTE	Sep 28 2024
R-4.4-mac	NOTE	Sep 28 2024
R-4.3-win	NOTE	Sep 28 2024
R-4.3-mac	NOTE	Sep 28 2024

Exports:addLabel aggTSE aggValue asLeaf asPhylo cbind changeTree colLinks colnames<-colTree colTree<-colTreeNames colTreeNames<-convertNode countLeaf countNode detectLoop distNode findAncestor findChild findDescendant findOS findSibling isLeaf joinNode LinkDataFrame makeTSE matTree printNode rbind referenceSeq referenceSeq<-resolveLoop rowLinks rownames<-rowTree rowTree<-rowTreeNames rowTreeNames<-shareNode showNode signalNode subsetByLeaf subsetByNode toTree trackNode transNode TreeSummarizedExperiment unionLeaf updateObject vertical_slot_names

Dependencies:abind ape askpass BH Biobase BiocGenerics BiocParallel Biostrings cli codetools cpp11 crayon curl DelayedArray digest dplyr fansi formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats mime nlme openssl pillar pkgconfig purrr R6 Rcpp rlang S4Arrays S4Vectors SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tidytree treeio UCSC.utils utf8 vctrs withr XVector yulab.utils zlibbioc

Introduction to TreeSummarizedExperiment

Ruizhu HUANG, Charlotte Soneson, Mark Robinson

Rendered fromIntroduction_to_treeSummarizedExperiment.Rmdusingknitr::rmarkdownon Sep 28 2024.

Last update: 2021-01-18
Started: 2018-12-12

Combine TreeSummarizedExperiment objects

Ruizhu HUANG, Charlotte Soneson, Mark Robinson

Rendered fromThe_combination_of_multiple_TSEs.Rmdusingknitr::rmarkdownon Sep 28 2024.

Last update: 2021-01-25
Started: 2021-01-17

Citation

Development and contributors

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