sigPathway: Pathway Analysis

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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 <wlai@alum.mit.edu>
License
GPL-2
Version
1.42.0
URLs

View on Bioconductor

Man 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.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

Files in this package

sigPathway/CHANGELOG
sigPathway/DESCRIPTION
sigPathway/NAMESPACE
sigPathway/R
sigPathway/R/calcGeneSetStat.R
sigPathway/R/calcProbeStat.R
sigPathway/R/checkInputs.R
sigPathway/R/estimateNumPerm.R
sigPathway/R/getPathwayStat.R
sigPathway/R/importGeneSets.R
sigPathway/R/rankPathways.R
sigPathway/R/runSigPathway.R
sigPathway/R/selectGeneSets.R
sigPathway/R/writeHTML.R
sigPathway/build
sigPathway/build/vignette.rds
sigPathway/data
sigPathway/data/MuscleExample.RData
sigPathway/inst
sigPathway/inst/doc
sigPathway/inst/doc/sigPathway-vignette.R
sigPathway/inst/doc/sigPathway-vignette.Rnw
sigPathway/inst/doc/sigPathway-vignette.pdf
sigPathway/man
sigPathway/man/MuscleExample.Rd
sigPathway/man/calcTNullFast.Rd
sigPathway/man/calcTStatFast.Rd
sigPathway/man/calculate.GSEA.Rd
sigPathway/man/calculate.NGSk.Rd
sigPathway/man/calculatePathwayStatistics.Rd
sigPathway/man/estimateNumPerm.Rd
sigPathway/man/getPathwayStatistics.NGSk.Rd
sigPathway/man/getPathwayStatistics.Rd
sigPathway/man/importGeneSets.Rd
sigPathway/man/rankPathways.NGSk.Rd
sigPathway/man/rankPathways.Rd
sigPathway/man/runSigPathway.Rd
sigPathway/man/selectGeneSets.Rd
sigPathway/man/writeSigPathway.Rd
sigPathway/src
sigPathway/src/Makevars
sigPathway/src/calc_gene_set_internal.c
sigPathway/src/calc_gene_set_stat.c
sigPathway/src/calc_probe_stat.c
sigPathway/src/calc_weights.c
sigPathway/src/matrix_fn.c
sigPathway/src/permute.c
sigPathway/src/shuffle.c
sigPathway/src/sigPathway.c
sigPathway/src/sigPathway.h
sigPathway/vignettes
sigPathway/vignettes/MHC1.png
sigPathway/vignettes/TopPathwaysTable.png
sigPathway/vignettes/sigPathway-vignette.Rnw
sigPathway/vignettes/sigPathway-vignette.bib