Pathway Analysis


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Documentation for package `sigPathway' version 1.1.4

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calcTNullFast Compute Null T Distribution for Each Gene
calcTStatFast Compute T-Statistics and Corresponding P-Values
calculate.GSEA Calculate 2-sided statistics based on the GSEA algorithm
calculate.NEk Calculate the NTk and NEk statistics
calculate.NGSk Calculate NGSk (NTk-like) statistics with gene label permutation
calculate.NTk Calculate the NTk and NEk statistics
estimateNumPerm Compute the Number of Unique Permutations for a Phenotype Vector
G Collection of Human Pathways from Gene Ontology, BioCyc, BioCarta, KEGG, and SuperArray
GenesetsU133a Collection of Human Pathways from Gene Ontology, BioCyc, BioCarta, KEGG, and SuperArray
getPathwayStatistics Give the statistics for the probe sets in a pathway
getPathwayStatistics.NGSk Give the statistics for the probe sets in a pathway
index.DM Inflammatory Myopathy Dataset
index.IBM Inflammatory Myopathy Dataset
index.NORM Inflammatory Myopathy Dataset
MuscleData Inflammatory Myopathy Dataset
rankPathways Summarizes Top Pathways from Pathway Analyses
rankPathways.NGSk Summarizes Top Pathways from One of the Pathway Analyses
runSigPathway Perform pathway analysis
selectGeneSets Select gene sets to be analyzed in pathway analysis
writeSigPathway Write results of pathway analysis to HTML format
writeSP Write results of pathway analysis to HTML format