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sigPathway (version 1.40.0)

Pathway Analysis

Description

Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005)

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Version

Version

1.40.0

License

GPL-2

Maintainer

Weil Lai

Last Published

February 15th, 2017

Functions in sigPathway (1.40.0)

calcTStatFast

Compute T-Statistics and Corresponding P-Values
importGeneSets

Import gene sets stored in GMT, GMX, GRP, and XML file formats
calculate.NGSk

Calculate NGSk (NTk-like) statistics with gene label permutation
writeSigPathway

Write results of pathway analysis to HTML format
getPathwayStatistics.NGSk

Give the statistics for the probe sets in a pathway
rankPathways

Summarizes Top Pathways from Pathway Analyses
calculate.GSEA

Calculate 2-sided statistics based on the GSEA algorithm
getPathwayStatistics

Give the statistics for the probe sets in a pathway
calcTNullFast

Compute Null T Distribution for Each Gene
selectGeneSets

Select gene sets to be analyzed in pathway analysis
rankPathways.NGSk

Summarizes Top Pathways from One of the Pathway Analyses
MuscleExample

Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway
calculatePathwayStatistics

Calculate the NTk and NEk statistics
runSigPathway

Perform pathway analysis
estimateNumPerm

Compute the Number of Unique Permutations for a Phenotype Vector