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"' |