# Package for Topology-based Pathway Analysis of RNASeq data

## Documentation for package ‘ToPASeq’ version 1.2.0

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

## Help Pages

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"'