# Pathway Analysis

## Documentation for package ‘sigPathway’ version 1.12.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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