Man pages for fionarhuang/TreeSummarizedExperiment
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

addLabeladd labels to nodes of a tree
aggTSEPerform data aggregations based on the available tree...
aggValuePerform data aggregations based on the available tree...
asLeafchange internal nodes to leaf nodes
asPhyloConvert a data frame to a phylo object
changeTreeChange the row or column tree
convertNodeTransfer between node number and node label
countLeafcount the number of leaf nodes
countNodecount the number of nodes
detectLoopDetect loops 'detectLoop' detects loops
distNodeCalculate the distance between any two nodes on the tree
dot-all_equal_in_listtest all elements in a list are equal
dot-all_have_DNAStringSettest all TSEs have DNAStringSet in the referenceSeq slot
dot-all_have_DNAStringSetListtest all TSEs have DNAStringSetList in the referenceSeq slot
dot-all_nonnull_in_listall elements in the list are NULL
dot-all_null_in_listall elements in the list are NULL
dot-any_null_in_listAny element in the list is NULL
dot-auto_rename_listrename a list automatically to avoid duplicated names
dot-bind_link_treebind links & trees when combine TSE
dot-is_equal_linkThe links & trees in the specified dim are consistent
dot-match_phylomatch a phylo to a list of phylo
dot-match_phylo_listmatch a list of phylo (x.phys) against to a list of phylo...
dot-match_x_dupYconvert char. indicator to num. indicator
dot-name_y_with_xname y with x
dot-numeric_ijconvert char. indicator to num. indicator
dot-rbind_refSeqrbind referenceSeq
dot-replace_link_tree_1dreplace row/col links & trees
dot-subset_leafupdate dimLinks and dimTree (used in subsetByLeaf)
dot-update_whichTreeupdate the 'whichTree' column in row/column link data
findAncestorFind the ancestors of specified nodes
findChildFind the children
findDescendantFind descendants (or offsprings)
findSiblingfind the sibling node
isLeafTo test whether the specified nodes are leaf nodes
joinNodeJoin nodes
LinkDataFrame-classLinkDataFrame: A S4 class extended from DataFrame An S4 class...
LinkDataFrame-constructorConstruct a LinkDataFrame Construct a LinkDataFrame object
makeTSEA toy TreeSummarizedExperiment object
matTreeTransform a phylo object into a matrix.
phylophylo: A S3 class for the phylogenetic tree
printNodeTo print out the node labels
resolveLoopResolve loops 'resolveLoop' resolve loops by adding suffix to...
shareNodeFind the share node
showNodeFind nodes on the tree
tinyTreeA simulated phylogenetic tree with 10 tips and 9 internal...
toTreeTranslate a data frame to a phylo object
trackNodetrack the nodes of a phylo tree
TreeeSummarizedExperiment-packageThe 'TreeSummarizedExperiment' package
TreeSummarizedExperiment-classAn S4 class TreeSummarizedExperiment
TreeSummarizedExperiment-combineCombine TSEs by rows or columns
TreeSummarizedExperiment-constructorConstruct a TreeSummarizedExperiment object
TreeSummarizedExperiment-internalTreeSummarizedExperiment internals
unionLeaflist leaf nodes that are the descendants of at least one...
updateObject-TreeSummarizedExperiment-methodUpdate a 'TreeSummarizedExperiment' object
fionarhuang/TreeSummarizedExperiment documentation built on Aug. 18, 2021, 12:15 p.m.