safe: Significance Analysis of Function and Expression

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.

Author
William T. Barry
Date of publication
None
Maintainer
William T. Barry <bbarry@jimmy.harvard.edu>
License
GPL (>= 2)
Version
3.14.0

View on Bioconductor

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

Files in this package

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