AGDEX: Agreement of Differential Expression Analysis
Version 1.24.0

A tool to evaluate agreement of differential expression for cross-species genomics

Browse man pages Browse package API and functions Browse package files

AuthorStan Pounds <stanley.pounds@stjude.org>; Cuilan Lani Gao <cuilan.gao@stjude.org>
Bioconductor views GeneExpression Genetics Microarray
Date of publicationNone
MaintainerCuilan lani Gao <cuilan.gao@stjude.org>
LicenseGPL Version 2 or later
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AGDEX")

Man pages

agdex: Agreement of Differential Expression Analysis
AGDEX-package: Agreement of differential expression analysis
agdex.res: Saved result returned by agdex()
agdex.scatterplot: scatter plot of AGDEX result
get.gset.result.details: Extract gene-level details from gene-set results
gset.data: a sample gene-set data
human.data: Sample ExpressionSet object of human data
make.dex.set.object: Make a list object for function agdex()
map.data: Probe-set Mapping Data
mouse.data: Mouse Data
read.agdex.gset.details: read detailed results of gene-set analyses
read.agdex.result: Read the output file of agdex analysis
write.agdex.gset.details: write the output of get.gset.result.details to a...
write.agdex.result: Write the AGDEX results to output file

Functions

AGDEX-package Man page
agdex Man page Source code
agdex.res Man page
agdex.scatterplot Man page Source code
all.assign.agdex Source code
choose.multinomial Source code
compute.agdex.stat Source code
compute.gset.agdex.stats Source code
compute.gset.dstats Source code
find.probe.col Source code
get.gset.result.details Man page Source code
gsc.to.index.list Source code
gset.data Man page
human.data Man page
make.dex.set.object Man page Source code
map.data Man page
map.gset.lists Source code
mouse.data Man page
prep.dex.set Source code
prep.map.data Source code
read.agdex.gset.details Man page Source code
read.agdex.gset.list Source code
read.agdex.result Man page Source code
read.enrich.gset.list Source code
read.gset.collection Source code
write.agdex.gset.details Man page Source code
write.agdex.result Man page Source code
write.gset.list.result Source code

Files

DESCRIPTION
NAMESPACE
R
R/agdex.R
R/agdex.scatterplot.R
R/all.assign.agdex.R
R/choose.multinomial.R
R/compute.agdex.stat.R
R/compute.gset.agdex.stats.R
R/compute.gset.dstats.R
R/find.probe.col.R
R/get.gset.result.details.R
R/gsc.to.index.list.R
R/make.dex.set.object.r
R/map.gset.lists.R
R/prep.dex.set.R
R/prep.map.data.R
R/read.agdex.gset.details.R
R/read.agdex.gset.list.R
R/read.agdex.result.R
R/read.enrich.gset.list.R
R/read.gset.collection.R
R/write.agdex.gset.details.R
R/write.agdex.result.R
R/write.gset.list.result.R
build
build/vignette.rds
data
data/agdex.res.rda
data/gset.data.rda
data/human.data.rda
data/map.data.rda
data/mouse.data.rda
inst
inst/doc
inst/doc/AGDEX.R
inst/doc/AGDEX.pdf
inst/doc/AGDEX.rnw
man
man/AGDEX-package.Rd
man/agdex.Rd
man/agdex.res.Rd
man/agdex.scatterplot.Rd
man/get.gset.result.details.Rd
man/gset.data.Rd
man/human.data.Rd
man/make.dex.set.object.Rd
man/map.data.Rd
man/mouse.data.Rd
man/read.agdex.gset.details.Rd
man/read.agdex.result.Rd
man/write.agdex.gset.details.Rd
man/write.agdex.result.Rd
vignettes
vignettes/AGDEX.rnw
AGDEX documentation built on May 20, 2017, 10:16 p.m.