Entry: MuscleExample
Aliases: MuscleExample tab phenotype G
Keywords: datasets
Description: Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway
URL: ../../../library/sigPathway/html/MuscleExample.html

Entry: calcTNullFast
Aliases: calcTNullFast
Keywords: array htest
Description: Compute Null T Distribution for Each Gene
URL: ../../../library/sigPathway/html/calcTNullFast.html

Entry: calcTStatFast
Aliases: calcTStatFast
Keywords: array htest
Description: Compute T-Statistics and Corresponding P-Values
URL: ../../../library/sigPathway/html/calcTStatFast.html

Entry: calculate.GSEA
Aliases: calculate.GSEA
Keywords: array htest
Description: Calculate 2-sided statistics based on the GSEA algorithm
URL: ../../../library/sigPathway/html/calculate.GSEA.html

Entry: calculate.NGSk
Aliases: calculate.NGSk
Keywords: array htest
Description: Calculate NGSk (NTk-like) statistics with gene label permutation
URL: ../../../library/sigPathway/html/calculate.NGSk.html

Entry: calculatePathwayStatistics
Aliases: calculate.NTk calculate.NEk
Keywords: array htest
Description: Calculate the NTk and NEk statistics
URL: ../../../library/sigPathway/html/calculatePathwayStatistics.html

Entry: estimateNumPerm
Aliases: estimateNumPerm
Keywords: array htest
Description: Compute the Number of Unique Permutations for a Phenotype Vector
URL: ../../../library/sigPathway/html/estimateNumPerm.html

Entry: getPathwayStatistics.NGSk
Aliases: getPathwayStatistics.NGSk
Keywords: array htest
Description: Give the statistics for the probe sets in a pathway
URL: ../../../library/sigPathway/html/getPathwayStatistics.NGSk.html

Entry: getPathwayStatistics
Aliases: getPathwayStatistics
Keywords: array htest
Description: Give the statistics for the probe sets in a pathway
URL: ../../../library/sigPathway/html/getPathwayStatistics.html

Entry: importGeneSets
Aliases: importGeneSets gmtToG gmxToG grpToG xmlToG
Keywords: file datagen
Description: Import gene sets stored in GMT, GMX, GRP, and XML file formats
URL: ../../../library/sigPathway/html/importGeneSets.html

Entry: rankPathways.NGSk
Aliases: rankPathways.NGSk
Keywords: array htest
Description: Summarizes Top Pathways from One of the Pathway Analyses
URL: ../../../library/sigPathway/html/rankPathways.NGSk.html

Entry: rankPathways
Aliases: rankPathways
Keywords: array htest
Description: Summarizes Top Pathways from Pathway Analyses
URL: ../../../library/sigPathway/html/rankPathways.html

Entry: runSigPathway
Aliases: runSigPathway
Keywords: array htest
Description: Perform pathway analysis
URL: ../../../library/sigPathway/html/runSigPathway.html

Entry: selectGeneSets
Aliases: selectGeneSets
Keywords: array htest
Description: Select gene sets to be analyzed in pathway analysis
URL: ../../../library/sigPathway/html/selectGeneSets.html

Entry: writeSigPathway
Aliases: writeSigPathway writeSP
Keywords: array htest
Description: Write results of pathway analysis to HTML format
URL: ../../../library/sigPathway/html/writeSigPathway.html
