Package for Topology-based Pathway Analysis of RNASeq data

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Documentation for package ‘ToPASeq’ version 1.0.1

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ToPASeq-package Package for topology-based pathway analysis of microarray and RNASeq data
AdjacencyMatrix2Pathway Function to coerce an adjacency matrix to a pathway
Clipper Function to use clipper method on microarray or RNA-Seq data
convertIdentifiersByVector Function to convert identifiers in pathways by user specified vector
defaultEdgeAttrs Auxiliary data needed for SPIA method
DEGraph Function to use DEGraph method on microarray or RNA-Seq data
degtable Function to extract parts of object
graphNEL2Pathway Function to coerce a graphNEL to a pathway
PWEA Function to use PWEA method on microarray or RNA-Seq data
reduceGraph Function to reduce the pathway graph
res Function to extract parts of object
SPIA Function to use SPIA method on microarray or RNA-Seq data
TAPPA Function to use TAPPA method on microarray or RNA-Seq data
TBS Function to use TBS 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