Package for Topology-based Pathway Analysis of RNASeq data

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Documentation for package ‘ToPASeq’ version 1.2.0

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ToPASeq-package Package for topology-based pathway analysis of microarray and RNASeq data
acc-method Class '"pathway"'
addEdge-method Class '"pathway"'
addNode-method Class '"pathway"'
AdjacencyMatrix2pathway Function to coerce an adjacency matrix to a pathway
changeDirection Class '"pathway"'
changeDirection-method Class '"pathway"'
changeInteraction Class '"pathway"'
changeInteraction-method Class '"pathway"'
clearNode-method Class '"pathway"'
Clipper Function to use clipper method on microarray or RNA-Seq data
collectWeightsPRS Function to calculate gene-level weights for topology-based pathway analysis
collectWeightsSPIA Function to calculate gene-level weights for topology-based pathway analysis
connComp-method Class '"pathway"'
convertIdentifiersByVector Function to convert identifiers in pathways by user specified vector
DEGraph Function to use DEGraph method on microarray or RNA-Seq data
degree-method Class '"pathway"'
degtable Function to extract parts of object
edgemode-method Class '"pathway"'
edgeNames-method Class '"pathway"'
edges-method Class '"pathway"'
estimateCF Function to estimate multi-subunit protein complexes and gene families in a pathway
graphNEL2pathway Function to coerce a graphNEL to a pathway
intersection-method Class '"pathway"'
isAdjacent-method Class '"pathway"'
isConnected-method Class '"pathway"'
isDirected-method Class '"pathway"'
join-method Class '"pathway"'
KEGG2pathway Function to parse KEGG KGML file into a pathway
makeDefaultEdgeData Creates auxiliary data needed for SPIA method
mostEdges-method Class '"pathway"'
nodes-method Class '"pathway"'
nodes<--method Class '"pathway"'
numEdges-method Class '"pathway"'
numNodes-method Class '"pathway"'
numNoEdges-method Class '"pathway"'
pathway-class Class '"pathway"'
preparePathways Function to prepare pathways for topology-based pathway analysis
prepareTIF Function to calculate gene-level weights for topology-based pathway analysis
PRS Function to use PRS method on microarray or RNA-Seq data
PWEA Function to use PWEA method on microarray or RNA-Seq data
reduceGraph Function to reduce the pathway graph
removeEdge-method Class '"pathway"'
removeNode-method Class '"pathway"'
res Function to extract parts of object
show-method Class '"pathway"'
SPIA Function to use SPIA method on microarray or RNA-Seq data
subGraph-method Class '"pathway"'
TAPPA Function to use TAPPA method on microarray or RNA-Seq data
ToPASeq Package for topology-based pathway analysis of microarray and RNASeq data
topo.sig Function to extract parts of object
TopologyGSA Function to use TopologyGSA method on microarray or RNA-Seq data
union-method Class '"pathway"'