Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005)
|Author||Weil Lai (optimized R and C code), Lu Tian and Peter Park (algorithm development and initial R code)|
|Date of publication||None|
|Maintainer||Weil Lai <firstname.lastname@example.org>|
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.NGSk: Calculate NGSk (NTk-like) statistics with gene label...
calculatePathwayStatistics: Calculate the NTk and NEk statistics
estimateNumPerm: Compute the Number of Unique Permutations for a Phenotype...
getPathwayStatistics: Give the statistics for the probe sets in a pathway
getPathwayStatistics.NGSk: Give the statistics for the probe sets in a pathway
importGeneSets: Import gene sets stored in GMT, GMX, GRP, and XML file...
MuscleExample: Subset of Inflammatory Myopathy Dataset to Demonstrate...
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