OGSA: Outlier Gene Set Analysis

OGSA provides a global estimate of pathway deregulation in cancer subtypes by integrating the estimates of significance for individual pathway members that have been identified by outlier analysis.

Author
Michael F. Ochs <ochsm@tcnj.edu>
Date of publication
None
Maintainer
Michael F. Ochs <ochsm@tcnj.edu>
License
GPL (== 2)
Version
1.4.0

View on Bioconductor

Man pages

cnv
Copy number variation data
copaInt
copaInt
copaIntE
copaIntE
copaStat
copaStat
expr
expr
expressionSetDataSet
expressionSetDataSet
expressionSetPheno
expressionSetPheno
meth
meth
OGSA-package
This package uses outlier statistics and gene set analysis to...
outCallRank
outCallRank
outCallRankE
outCallRankE
outCallTib
outCallTib
outCallTibE
outCallTibE
outCount
outCount
outMap
outMap
outRank
outRank
pathGS
Gene set defined by BioCarta pathway
pheno
pheno
testGScogps
testGScogps

Files in this package

OGSA/DESCRIPTION
OGSA/NAMESPACE
OGSA/R
OGSA/R/OutCallTibE.R
OGSA/R/copaInt.R
OGSA/R/copaIntE.R
OGSA/R/copaStat.R
OGSA/R/expressionSetDataSet.R
OGSA/R/expressionSetPheno.R
OGSA/R/outCallRank.R
OGSA/R/outCallRankE.R
OGSA/R/outCallTib.R
OGSA/R/outCount.R
OGSA/R/outMap.R
OGSA/R/outRank.R
OGSA/R/testGScogps.R
OGSA/build
OGSA/build/vignette.rds
OGSA/data
OGSA/data/ExampleData.rda
OGSA/data/KEGG_BC_GS.rda
OGSA/data/datalist
OGSA/inst
OGSA/inst/NEWS.txt
OGSA/inst/doc
OGSA/inst/doc/OGSAUsersManual.R
OGSA/inst/doc/OGSAUsersManual.Rnw
OGSA/inst/doc/OGSAUsersManual.pdf
OGSA/man
OGSA/man/OGSA-package.Rd
OGSA/man/cnv.Rd
OGSA/man/copaInt.Rd
OGSA/man/copaIntE.Rd
OGSA/man/copaStat.Rd
OGSA/man/expr.Rd
OGSA/man/expressionSetDataSet.Rd
OGSA/man/expressionSetPheno.Rd
OGSA/man/meth.Rd
OGSA/man/outCallRank.Rd
OGSA/man/outCallRankE.Rd
OGSA/man/outCallTib.Rd
OGSA/man/outCallTibE.Rd
OGSA/man/outCount.Rd
OGSA/man/outMap.Rd
OGSA/man/outRank.Rd
OGSA/man/pathGS.Rd
OGSA/man/pheno.Rd
OGSA/man/testGScogps.Rd
OGSA/vignettes
OGSA/vignettes/OGSAUsersManual.Rnw
OGSA/vignettes/OGSA_Fig_1.png
OGSA/vignettes/chicago.sty