Package: genefilter 1.95.0
Bioconductor Package Maintainer
genefilter: genefilter: methods for filtering genes from high-throughput experiments
Some basic functions for filtering genes.
Authors:
genefilter_1.95.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
genefilter/json (API)
NEWS
| # Install 'genefilter' in R: |
| install.packages('genefilter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- tdata - A small test dataset of Affymetrix Expression data.
On BioConductor:genefilter-1.95.0(bioc 3.24)genefilter-1.94.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:4f08f4ca16. Checks:12 WARNING, 2 OK. Indexed: yes.
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| bioc-checks | WARNING | 179 | ||
| linux-devel-arm64 | WARNING | 229 | ||
| linux-devel-x86_64 | WARNING | 281 | ||
| source / vignettes | OK | 296 | ||
| linux-release-arm64 | WARNING | 258 | ||
| linux-release-x86_64 | WARNING | 320 | ||
| macos-release-arm64 | WARNING | 191 | ||
| macos-release-x86_64 | WARNING | 345 | ||
| macos-oldrel-arm64 | WARNING | 156 | ||
| macos-oldrel-x86_64 | WARNING | 315 | ||
| windows-devel | WARNING | 209 | ||
| windows-release | WARNING | 211 | ||
| windows-oldrel | WARNING | 227 | ||
| wasm-release | OK | 181 |
Exports:AnovaareaAUCcolFtestscolttestscoxfiltercvdist2eSetFilterfastTfeatureFilterfilter_volcanofiltered_pfiltered_RfilterfunfindLargestgapFiltergenefiltergenefindergenescalegetFilterNamesgetFuncDescgetRdAsTexthalf.range.modeisESetkappa_pkappa_tkOverAmaxAnsFilterparseArgsparseDescpAUCplotpOverArejection_plotrowFtestsrowpAUCsrowSdsrowttestsrowVarssenssetESetArgsshorthshowshowESetspecttestvarFilter
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsgluehttrIRangesjsonliteKEGGRESTlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfosurvivalsysvctrsXMLxtableXVector
How to find genes whose expression profile is similar to that of specified genes
Rendered fromhowtogenefinder.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2023-03-16
Started: 2023-03-16
03 - Additional plots for: Independent filtering increases power for detecting differentially expressed genes, Bourgon et al., PNAS (2010)
Rendered fromindependent_filtering_plots.Rnwusingknitr::knitron May 30 2026.Last update: 2021-01-14
Started: 2013-10-25
Using the genefilter function to filter genes from a microarray dataset
Rendered fromhowtogenefilter.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2023-03-28
Started: 2023-03-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A filter function for Analysis of Variance | Anova |
| A filter function for univariate Cox regression. | coxfilter |
| A filter function for the coefficient of variation. | cv |
| Calculate an n-by-n matrix by applying a function to all pairs of columns of an m-by-n matrix. | dist2 |
| A function to filter an eSet object | eSetFilter getFilterNames getFuncDesc getRdAsText isESet parseArgs parseDesc setESetArgs showESet |
| Volcano plot for overall variance filtering | filter_volcano |
| Compute and adjust p-values, with filtering | filtered_p filtered_R |
| Creates a first FALSE exiting function from the list of filter functions it is given. | filterfun |
| Find the Entrez Gene ID corresponding to the largest statistic | findLargest |
| A filter to select genes based on there being a gap. | gapFilter |
| A function to filter genes. | genefilter |
| Deprecated functions in package 'genefilter' | genefilter-deprecated |
| Finds genes that have similar patterns of expression. | genefinder genefinder,ExpressionSet,vector-method genefinder,matrix,vector-method |
| Scales a matrix or vector. | genescale |
| Mode estimation for continuous data | half.range.mode |
| Compute proportionality constant for fold change bound. | kappa_p kappa_t |
| A filter function for k elements larger than A. | kOverA |
| A filter function to filter according to the maximum. | maxA |
| Filtering of Features in an ExpressionSet | featureFilter nsFilter nsFilter,ExpressionSet-method varFilter |
| A filter function to filter according to the proportion of elements larger than A. | pOverA |
| Plot rejections vs. p-value cutoff | rejection_plot |
| t-tests and F-tests for rows or columns of a matrix | colFtests colFtests,ExpressionSet,character-method colFtests,ExpressionSet,factor-method colFtests,matrix,factor-method colttests colttests,ExpressionSet,character-method colttests,ExpressionSet,factor-method colttests,ExpressionSet,missing-method colttests,matrix,factor-method colttests,matrix,missing-method fastT rowFtests rowFtests,ExpressionSet,character-method rowFtests,ExpressionSet,factor-method rowFtests,matrix,factor-method rowttests rowttests,ExpressionSet,character-method rowttests,ExpressionSet,factor-method rowttests,ExpressionSet,missing-method rowttests,matrix,factor-method rowttests,matrix,missing-method |
| Rowwise ROC and pAUC computation | rowpAUCs rowpAUCs,ExpressionSet,ANY-method rowpAUCs,ExpressionSet,character-method rowpAUCs,matrix,factor-method rowpAUCs,matrix,numeric-method rowpAUCs-methods |
| Class "rowROC" | area area,rowROC-method AUC AUC,rowROC-method pAUC pAUC,rowROC,numeric-method plot,rowROC,missing-method rowROC rowROC-class sens sens,rowROC-method show,rowROC-method spec spec,rowROC-method [,rowROC,ANY,ANY,ANY-method |
| Row variance and standard deviation of a numeric array | rowSds rowVars |
| A location estimator based on the shorth | shorth |
| A small test dataset of Affymetrix Expression data. | tdata |
| A filter function for a t.test | ttest |
