Package: treeclimbR 1.1.0

Charlotte Soneson

treeclimbR: An algorithm to find optimal signal levels in a tree

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Authors:Ruizhu Huang [aut], Charlotte Soneson [aut, cre]

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NEWS

# Install 'treeclimbR' in R:

install.packages('treeclimbR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/csoneson/treeclimbr/issues

On BioConductor:treeclimbR-1.1.0(bioc 3.20)treeclimbR-1.0.0(bioc 3.19)

bioconductor-package

26 exports 1.24 score 156 dependencies

Last updated 2 months agofrom:3c3e1a3d46

Exports:aggDS buildTree calcMediansByTreeMarker calcTreeCounts calcTreeMedians edgerWrp evalCand fdr findChild findExcl getCand getData getLevel infoCand isConnect medianByClusterMarker nodeResult parEstimate runDA runDS selNode simData topNodes tpr TreeHeatmap treeScore

Dependencies:abind ALL ape aplot askpass backports BH Biobase BiocGenerics BiocParallel Biostrings boot broom cachem car carData circlize cli clue cluster codetools colorRamps colorspace ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon curl cytolib DelayedArray diffcyt digest dirmult doParallel dplyr edgeR fansi farver fastmap flowCore FlowSOM foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtree GlobalOptions glue gridExtra gridGraphics gtable httr igraph IRanges isoband iterators jsonlite labeling lambda.r lattice lazyeval lifecycle limma lme4 locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa multcomp munsell mvtnorm nlme nloptr nnet numDeriv openssl patchwork pbkrtest pillar pkgconfig plyr png polyclip polynom purrr quantreg R6 RColorBrewer Rcpp RcppEigen reshape2 Rhdf5lib rjson rlang RProtoBufLib rstatix Rtsne S4Arrays S4Vectors sandwich scales shape SingleCellExperiment snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts TH.data tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment tweenr UCSC.utils utf8 vctrs viridis viridisLite withr XML XVector yulab.utils zlibbioc zoo

Finding optimal resolution of hierarchical hypotheses with treeclimbR

Charlotte Soneson and Ruizhu Huang

Rendered fromtreeclimbR.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2024-03-10
Started: 2024-02-10

Help page	Topics
Aggregate observed data based on a tree	aggDS
Tree versions of diffcyt functions	buildTree calcMediansByTreeMarker calcTreeCounts calcTreeMedians diffcyt_workflow
Wrapper applying an edgeR differential analysis workflow	edgerWrp
Evaluate candidate levels and select the optimal one	evalCand
Calculate false discovery rate (FDR) on a tree structure	fdr
Find the children of an internal node in a tree	findChild
Find branches that are non-overlapping with specified branches in a tree	findExcl
Generate candidates for different thresholds	getCand
Extract data from a TreeHeatmap	getData
Search for a target level on the tree via a specified score	getLevel
Get information of candidates	infoCand
Check whether nodes are contained in the same path from a leaf to the root in a tree	isConnect
Calculate median values of markers for each cluster	medianByClusterMarker
Extract table with node-level DA/DS results	nodeResult
Parameter estimation for Dirichlet-multinomial distribution	parEstimate
Test for differential abundance using edgeR	runDA
Test for differential state using edgeR	runDS
Select branches meeting certain criteria	selNode
Simulate different scenarios of abundance change in entities	simData
Generate a table of top-ranked entities (nodes)	topNodes
Calculate true positive rate (TPR) on a tree structure	tpr
Generate a heatmap corresponding to an arbitrary aggregation level of a tree	TreeHeatmap
Generate weighted tree score accounting for the family effect	treeScore

Package: treeclimbR 1.1.0

treeclimbR: An algorithm to find optimal signal levels in a tree

Finding optimal resolution of hierarchical hypotheses with treeclimbR

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