genefilter: genefilter: methods for filtering genes from high-throughput experiments

Some basic functions for filtering genes

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genefilter")
AuthorR. Gentleman, V. Carey, W. Huber, F. Hahne
Bioconductor views Microarray
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.58.0

View on Bioconductor

Man pages

Functions

Anova Man page
area Man page
area,rowROC-method Man page
AUC Man page
AUC,rowROC-method Man page
colFtests Man page
colFtests,ExpressionSet,character-method Man page
colFtests,ExpressionSet,factor-method Man page
colFtests,matrix,factor-method Man page
colttests Man page
colttests,ExpressionSet,character-method Man page
colttests,ExpressionSet,factor-method Man page
colttests,ExpressionSet,missing-method Man page
colttests,matrix,factor-method Man page
colttests,matrix,missing-method Man page
coxfilter Man page
cv Man page
dist2 Man page
eSetFilter Man page
fastT Man page
featureFilter Man page
filtered_p Man page
filtered_R Man page
filterfun Man page
filter_volcano Man page
findLargest Man page
gapFilter Man page
genefilter Man page
genefinder Man page
genefinder,ExpressionSet,vector-method Man page
genefinder,matrix,vector-method Man page
genescale Man page
getFilterNames Man page
getFuncDesc Man page
getRdAsText Man page
half.range.mode Man page
isESet Man page
kappa_p Man page
kappa_t Man page
kOverA Man page
maxA Man page
nsFilter Man page
nsFilter,ExpressionSet-method Man page
parseArgs Man page
parseDesc Man page
pAUC Man page
pAUC,rowROC,numeric-method Man page
plot,rowROC,missing-method Man page
pOverA Man page
rejection_plot Man page
rowFtests Man page
rowFtests,ExpressionSet,character-method Man page
rowFtests,ExpressionSet,factor-method Man page
rowFtests,matrix,factor-method Man page
rowpAUCs Man page
rowpAUCs,ExpressionSet,ANY-method Man page
rowpAUCs,ExpressionSet,character-method Man page
rowpAUCs,matrix,factor-method Man page
rowpAUCs,matrix,numeric-method Man page
rowpAUCs-methods Man page
rowROC Man page
rowROC-class Man page
[,rowROC-method Man page
rowSds Man page
rowttests Man page
rowttests,ExpressionSet,character-method Man page
rowttests,ExpressionSet,factor-method Man page
rowttests,ExpressionSet,missing-method Man page
rowttests,matrix,factor-method Man page
rowttests,matrix,missing-method Man page
rowVars Man page
sens Man page
sens,rowROC-method Man page
setESetArgs Man page
shorth Man page
showESet Man page
show,rowROC-method Man page
spec Man page
spec,rowROC-method Man page
tdata Man page
ttest Man page
varFilter Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/all.R R/dist2.R R/eSetFilter.R R/fastT.R R/filter_volcano.R R/filtered_p.R R/genefinder.R R/half.range.mode.R R/kappa_p.R R/nsFilter.R R/rejection_plot.R R/rowROC-accessors.R R/rowSds.R R/rowpAUCs-methods.R R/rowttests-methods.R R/shorth.R R/zzz.R
build
build/vignette.rds
data
data/tdata.R
docs
docs/Cluster.pdf
docs/gcluster.tex
docs/gfilter.tex
inst
inst/doc
inst/doc/howtogenefilter.R
inst/doc/howtogenefilter.Rnw
inst/doc/howtogenefilter.pdf
inst/doc/howtogenefinder.R
inst/doc/howtogenefinder.Rnw
inst/doc/howtogenefinder.pdf
inst/doc/independent_filtering.R
inst/doc/independent_filtering.Rnw
inst/doc/independent_filtering.pdf
inst/doc/independent_filtering_plots.R
inst/doc/independent_filtering_plots.Rnw
inst/doc/independent_filtering_plots.pdf
inst/wFun
inst/wFun/Anova.xml
inst/wFun/coxfilter.xml
inst/wFun/cv.xml
inst/wFun/gapFilter.xml
inst/wFun/kOverA.xml
inst/wFun/maxA.xml
inst/wFun/pOverA.xml
inst/wFun/ttest.xml
man
man/Anova.Rd man/coxfilter.Rd man/cv.Rd man/dist2.Rd man/eSetFilter.Rd man/filter_volcano.Rd man/filtered_p.Rd man/filterfun.Rd man/findLargest.Rd man/gapFilter.Rd man/genefilter.Rd man/genefinder.Rd man/genescale.Rd man/half.range.mode.Rd man/kOverA.Rd man/kappa_p.Rd man/maxA.Rd man/nsFilter.Rd man/pOverA.Rd man/rejection_plot.Rd man/rowFtests.Rd man/rowROC-class.Rd man/rowSds.Rd man/rowpAUCs.Rd man/shorth.Rd man/tdata.Rd man/ttest.Rd
src
src/genefilter.h
src/half_range_mode.cpp
src/init.c
src/nd.c
src/pAUC.c
src/rowPAUCs.c
src/rowttests.c
src/ttest.f
vignettes
vignettes/howtogenefilter.Rnw
vignettes/howtogenefinder.Rnw
vignettes/independent_filtering.Rnw
vignettes/independent_filtering_plots.Rnw
vignettes/library.bib

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