An algorithm to find optimal signal levels in a tree

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Documentation for package ‘treeclimbR’ version 1.3.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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