safe: Significance Analysis of Function and Expression
Version 3.16.0

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

AuthorWilliam T. Barry
Bioconductor views DifferentialExpression GeneSetEnrichment Pathways Software StatisticalMethod
Date of publicationNone
MaintainerWilliam T. Barry <bbarry@jimmy.harvard.edu>
LicenseGPL (>= 2)
Version3.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("safe")

Getting started

Package overview

Popular man pages

getCmatrix: Generation of a C matrix
p53.stat: p53 Mutation Status
SAFE-class: Class SAFE
safedag: SAFE results displayed in Gene Ontology
safe-internal: Internal SAFE functions
safeplot: SAFE plot
safe.toptable: Category-specific results from SAFE
See all...

All man pages Function index File listing

Man pages

gene.results: Gene-specific results from SAFE
getCmatrix: Generation of a C matrix
p53.stat: p53 Mutation Status
safe: Significance Analysis of Function and Expression
SAFE-class: Class SAFE
safedag: SAFE results displayed in Gene Ontology
safe-internal: Internal SAFE functions
safe-package: Significance Analysis of Function and Expression
safeplot: SAFE plot
safe.toptable: Category-specific results from SAFE

Functions

SAFE-class Man page
[,SAFE-method Man page
error.FDR.BH Man page Source code
error.FDR.YB Man page Source code
error.FWER.Bonf Man page Source code
error.FWER.Holm Man page Source code
error.FWER.WY Man page Source code
gene.results Man page Source code
getCOXresiduals Man page Source code
getCmatrix Man page Source code
getPIcomplete Man page Source code
getPImatrix Man page Source code
getXYresiduals Man page Source code
global.AveDiff Man page Source code
global.Fisher Man page Source code
global.Kolmogorov Man page Source code
global.Pearson Man page Source code
global.Wilcoxon Man page Source code
local.f.ANOVA Man page Source code
local.t.LM Man page Source code
local.t.Student Man page Source code
local.t.Welch Man page Source code
local.t.paired Man page Source code
p53.stat Man page
safe Man page Source code
safe-package Man page
safe.toptable Man page Source code
safedag Man page Source code
safeplot Man page Source code
show,SAFE-method Man page
sigfig Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/SAFE-class.R
R/error.FDR.BH.R
R/error.FDR.YB.R
R/error.FWER.Bonf.R
R/error.FWER.Holm.R
R/error.FWER.WY.R
R/gene.results.R
R/getCOXresiduals.R
R/getCmatrix.R
R/getPIcomplete.R
R/getPImatrix.R
R/getXYresiduals.R
R/global.AveDiff.R
R/global.Fisher.R
R/global.Kolmogorov.R
R/global.Pearson.R
R/global.Wilcoxon.R
R/local.f.ANOVA.R
R/local.t.LM.R
R/local.t.Student.R
R/local.t.Welch.R
R/local.t.paired.R
R/safe.R
R/safe.toptable.R
R/safedag.R
R/safeplot.R
R/sigfig.R
build
build/vignette.rds
data
data/p53.stat.rda
inst
inst/doc
inst/doc/SAFEmanual3.R
inst/doc/SAFEmanual3.Rnw
inst/doc/SAFEmanual3.pdf
man
man/SAFE-class.Rd
man/gene.results.Rd
man/getCmatrix.Rd
man/p53.stat.Rd
man/safe-internal.Rd
man/safe-package.Rd
man/safe.Rd
man/safe.toptable.Rd
man/safedag.Rd
man/safeplot.Rd
vignettes
vignettes/SAFEmanual3-DAG1.pdf
vignettes/SAFEmanual3-DAG2.pdf
vignettes/SAFEmanual3-parallel.pdf
vignettes/SAFEmanual3.Rnw
safe documentation built on May 20, 2017, 10:53 p.m.

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