Package index

All functions

TreeHeatmap()

Generate a heatmap corresponding to an arbitrary aggregation level of a tree

aggDS()

Aggregate observed data based on a tree

buildTree() calcMediansByTreeMarker() calcTreeCounts() calcTreeMedians()

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

treeScore()

Generate weighted tree score accounting for the family effect