SAGx: Statistical Analysis of the GeneChip
Version 1.50.0

A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.

Browse man pages Browse package API and functions Browse package files

AuthorPer Broberg
Bioconductor views Clustering DataImport DifferentialExpression GeneExpression GeneSetEnrichment KEGG Microarray MultipleComparison OneChannel Pathways Preprocessing Regression
Date of publicationNone
MaintainerPer Broberg, <pi.broberg@gmail.com>
LicenseGPL-3
Version1.50.0
URL http://home.swipnet.se/pibroberg/expression_hemsida1.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("SAGx")

Man pages

clin2mim: Output a script file to WinMIM, linking clinical data and...
cluster.q: Clustering Goodness measured by Q2
estimatep0: Estimate proportion unchanged genes
fetchSignal: Fetch data from the GATC database
firstpass: First pass description of GeneChip data
fom: Clustering Figure of Merit
fp.fn: Calculation of fp and fn based on a vector of p-values
Fstat: Calculation of F statistic by gene given a linear model
gap: GAP statistic clustering figure of merit
GSEA.mean.t: Gene Set Enrichment Analysis using output from samroc
JT.test: Jonckheere-Terpstra trend test
list.experiments: Display all experiment names and id's
list.intersection.p: p-value for intersection of two gene lists.
mat2TeX: Ouput matrix to LaTeX
myclus: A clustering function
normalise: Normalise arrays
one.probeset.per.gene: Select the best probeset per gene
outlier: Identify outliers in the multivariate distribution
p0.mom: Estimate proportion unchanged genes
pava: Pooling of Adjacent Violators
pava.fdr: Estimate of the FDR and the proportion unchanged genes
R2BASE: Produces a BASE file
R2mim: Output a script file to WinMIM
rank.genes: Rank genes with respect to multiple criteria
rank.trend: Trend analysis based on ranks
rsd.test: Compare two groups with respect to their RSD (CV)
samrocn: Calculate ROC curve based SAM statistic
samrocnboot: Calculate ROC curve based SAM statistic
samroc.result-class: Class "samroc.result" for results of the function samrocN
union.of.pways: Create the union of two pathway lists
Xprep: Fitting of a linear model
Xprep.resid: Calculation of input of residuals from linear model

Functions

Fstat Man page Source code
GSEA.mean.t Man page Source code
JT.test Man page Source code
R2BASE Man page Source code
R2mim Man page Source code
Xprep Man page Source code
Xprep.resid Man page Source code
clin2mim Man page Source code
cluster.q Man page Source code
estimatep0 Man page Source code
fetchSignal Man page Source code
firstpass Man page Source code
fom Man page Source code
fp.fn Man page Source code
gap Man page Source code
list.experiments Man page Source code
list.intersection.p Man page Source code
mat2TeX Man page Source code
myclus Man page Source code
normalise Man page Source code
onLoad Source code
one.probeset.per.gene Man page Source code
outlier Man page Source code
p0.mom Man page Source code
pava Man page Source code
pava.fdr Man page Source code
plot,samroc.result,ANY-method Man page
plot,samroc.result-method Man page
rank.genes Man page Source code
rank.trend Man page Source code
rsd.test Man page Source code
samroc.result-class Man page
samrocN Man page Source code
samrocNboot Man page Source code
show,samroc.result-method Man page
union.of.pways Man page Source code

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/Fstat.r
R/GSEA.mean.t.R
R/JT.test.r
R/R2BASE.R
R/R2mim.r
R/Xprep.r
R/Xprep.resid.R
R/clin2mim.r
R/cluster.q.r
R/estimatep0.r
R/fetchSignal.r
R/firstpass.r
R/fom.r
R/fp.fn.r
R/gap.r
R/internal.R
R/list.experiments.r
R/list.intersection.p.r
R/mat2TeX.r
R/myclus.r
R/normalise.r
R/one.probeset.per.gene.R
R/outlier.r
R/p0.mom.r
R/pava.fdr.r
R/pava.r
R/rank.genes.R
R/rank.trend.r
R/rsd.test.r
R/samrocN.r
R/samrocNboot.r
R/samrocresult.R
R/union.of.pways.R
build
build/vignette.rds
inst
inst/doc
inst/doc/samroc-ex.R
inst/doc/samroc-ex.Rnw
inst/doc/samroc-ex.pdf
man
man/Fstat.rd
man/GSEA.mean.t.rd
man/JT.test.rd
man/R2BASE.rd
man/R2mim.rd
man/Xprep.rd
man/Xprep.resid.rd
man/clin2mim.rd
man/cluster.q.rd
man/estimatep0.rd
man/fetchSignal.rd
man/firstpass.rd
man/fom.rd
man/fp.fn.rd
man/gap.rd
man/list.experiments.rd
man/list.intersection.p.rd
man/mat2TeX.rd
man/myclus.rd
man/normalise.rd
man/one.probeset.per.gene.rd
man/outlier.rd
man/p0.mom.rd
man/pava.fdr.rd
man/pava.rd
man/rank.genes.rd
man/rank.trend.rd
man/rsd.test.rd
man/samroc.result-class.rd
man/samrocn.rd
man/samrocnboot.rd
man/union.of.pways.rd
src
src/minigsea.c
src/newboot.c
src/samrocNboot.c
test
vignettes
vignettes/samroc-ex.Rnw
vignettes/samroc-ex.bib
SAGx documentation built on May 20, 2017, 10:18 p.m.