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

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Some basic functions for filtering genes

Author
R. Gentleman, V. Carey, W. Huber, F. Hahne
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.56.0

View on Bioconductor

Man pages

Anova
A filter function for Analysis of Variance
coxfilter
A filter function for univariate Cox regression.
cv
A filter function for the coefficient of variation.
dist2
Calculate an n-by-n matrix by applying a function to all...
eSetFilter
A function to filter an eSet object
filtered_p
Compute and adjust p-values, with filtering
filterfun
Creates a first FALSE exiting function from the list of...
filter_volcano
Volcano plot for overall variance filtering
findLargest
Find the Entrez Gene ID corresponding to the largest...
gapFilter
A filter to select genes based on there being a gap.
genefilter
A function to filter genes.
genefinder
Finds genes that have similar patterns of expression.
genescale
Scales a matrix or vector.
half.range.mode
Mode estimation for continuous data
kappa_p
Compute proportionality constant for fold change bound.
kOverA
A filter function for k elements larger than A.
maxA
A filter function to filter according to the maximum.
nsFilter
Filtering of Features in an ExpressionSet
pOverA
A filter function to filter according to the proportion of...
rejection_plot
Plot rejections vs. p-value cutoff
rowFtests
t-tests and F-tests for rows or columns of a matrix
rowpAUCs
Rowwise ROC and pAUC computation
rowROC-class
Class "rowROC"
rowSds
Row variance and standard deviation of a numeric array
shorth
A location estimator based on the shorth
tdata
A small test dataset of Affymetrix Expression data.
ttest
A filter function for a t.test

Files in this package

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