sigPathway: Pathway Analysis
Version 1.44.1

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

Browse man pages Browse package API and functions Browse package files

AuthorWeil Lai (optimized R and C code), Lu Tian and Peter Park (algorithm development and initial R code)
Bioconductor views DifferentialExpression MultipleComparison
Date of publicationNone
MaintainerWeil Lai <wlai@alum.mit.edu>
LicenseGPL-2
Version1.44.1
URL http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102 http://www.chip.org/~ppark/Supplements/PNAS05.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sigPathway")

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

Functions

G Man page
MuscleExample Man page
calcSP Source code
calcTNullFast Man page Source code
calcTStatFast Man page Source code
calculate.GSEA Man page Source code
calculate.NEk Man page Source code
calculate.NGSk Man page Source code
calculate.NTk Man page Source code
checkInputs.annotpkg Source code
checkInputs.gsList Source code
checkInputs.nsim Source code
checkInputs.phenotype.ngroups Source code
checkInputs.tab.phenotype.ngroups Source code
convertDF2HTML Source code
estimateNumPerm Man page Source code
getPathwayStatistics Man page Source code
getPathwayStatistics.NGSk Man page Source code
gmtToG Man page Source code
gmxToG Man page Source code
grpToG Man page Source code
importGeneSets Man page Source code
phenotype Man page
rankPathways Man page Source code
rankPathways.NGSk Man page Source code
runSigPathway Man page Source code
selectGeneSets Man page Source code
tab Man page
writeSP Man page Source code
writeSigPathway Man page Source code
xmlToG Man page Source code

Files

CHANGELOG
DESCRIPTION
NAMESPACE
R
R/calcGeneSetStat.R
R/calcProbeStat.R
R/checkInputs.R
R/estimateNumPerm.R
R/getPathwayStat.R
R/importGeneSets.R
R/rankPathways.R
R/runSigPathway.R
R/selectGeneSets.R
R/writeHTML.R
build
build/vignette.rds
data
data/MuscleExample.RData
inst
inst/doc
inst/doc/sigPathway-vignette.R
inst/doc/sigPathway-vignette.Rnw
inst/doc/sigPathway-vignette.pdf
man
man/MuscleExample.Rd
man/calcTNullFast.Rd
man/calcTStatFast.Rd
man/calculate.GSEA.Rd
man/calculate.NGSk.Rd
man/calculatePathwayStatistics.Rd
man/estimateNumPerm.Rd
man/getPathwayStatistics.NGSk.Rd
man/getPathwayStatistics.Rd
man/importGeneSets.Rd
man/rankPathways.NGSk.Rd
man/rankPathways.Rd
man/runSigPathway.Rd
man/selectGeneSets.Rd
man/writeSigPathway.Rd
src
src/Makevars
src/calc_gene_set_internal.c
src/calc_gene_set_stat.c
src/calc_probe_stat.c
src/calc_weights.c
src/matrix_fn.c
src/permute.c
src/shuffle.c
src/sigPathway.c
src/sigPathway.h
vignettes
vignettes/MHC1.png
vignettes/TopPathwaysTable.png
vignettes/sigPathway-vignette.Rnw
vignettes/sigPathway-vignette.bib
sigPathway documentation built on May 20, 2017, 9:42 p.m.