Pathway Analysis


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Documentation for package ‘sigPathway’ version 1.8.0

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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 Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway
getPathwayStatistics Give the statistics for the probe sets in a pathway
getPathwayStatistics.NGSk Give the statistics for the probe sets in a pathway
gmtToG Import gene sets stored in GMT, GMX, GRP, and XML file formats
gmxToG Import gene sets stored in GMT, GMX, GRP, and XML file formats
grpToG Import gene sets stored in GMT, GMX, GRP, and XML file formats
importGeneSets Import gene sets stored in GMT, GMX, GRP, and XML file formats
MuscleExample Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway
phenotype Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway
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
tab Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway
writeSigPathway Write results of pathway analysis to HTML format
writeSP Write results of pathway analysis to HTML format
xmlToG Import gene sets stored in GMT, GMX, GRP, and XML file formats