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 |
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 |