Package: genefilter 1.89.0
Bioconductor Package Maintainer
genefilter: genefilter: methods for filtering genes from high-throughput experiments
Some basic functions for filtering genes.
Authors:
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genefilter.pdf |genefilter.html✨
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-1.89.0(bioc 3.21)genefilter-1.88.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:46934e9a8e. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 18 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 18 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 18 2024 |
Exports:AnovaareaAUCcolFtestscolttestscoxfiltercvdist2eSetFilterfastTfeatureFilterfilter_volcanofiltered_pfiltered_RfilterfunfindLargestgapFiltergenefiltergenefindergenescalegetFilterNamesgetFuncDescgetRdAsTexthalf.range.modeisESetkappa_pkappa_tkOverAmaxAnsFilterparseArgsparseDescpAUCplotpOverArejection_plotrowFtestsrowpAUCsrowSdsrowttestsrowVarssenssetESetArgsshorthshowshowESetspecttestvarFilter
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorssurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
How to find genes whose expression profile is similar to that of specified genes
Rendered fromhowtogenefinder.Rmdusingknitr::rmarkdownon Dec 18 2024.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 Dec 18 2024.Last update: 2021-01-14
Started: 2013-10-25
Using the genefilter function to filter genes from a microarray dataset
Rendered fromhowtogenefilter.Rmdusingknitr::rmarkdownon Dec 18 2024.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 |
