Package: BiocGenerics 0.53.0

Hervé Pagès

BiocGenerics: S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Authors:The Bioconductor Dev Team

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NEWS

# Install 'BiocGenerics' in R:
install.packages('BiocGenerics', repos = c('https://mojaveazure.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/biocgenerics/issues

On BioConductor:BiocGenerics-0.51.3(bioc 3.20)BiocGenerics-0.50.0(bioc 3.19)

infrastructurebioconductor-packagecore-package

10.92 score 12 stars 2.2k packages 494 scripts 128 exports 0 dependencies

Last updated 12 hours agofrom:441e44734f. Checks:OK: 1 ERROR: 5 WARNING: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winERROROct 29 2024
R-4.5-linuxWARNINGOct 29 2024
R-4.4-winERROROct 29 2024
R-4.4-macERROROct 29 2024
R-4.3-winERROROct 29 2024
R-4.3-macERROROct 29 2024

Exports:%in%annotationannotation<-anyDuplicatedapermappendas.data.frameas.listas.vectorbasenamebasename<-boxplotcbindcolnamescolnames<-combineconditionsconditions<-containsOutOfMemoryDatacountscounts<-dbconndbfiledensitydesigndesign<-dimsdirnamedirname<-dispTabledispTable<-do.callduplicatedendend<-estimateDispersionsestimateSizeFactorsevalevalqfileNameFilterFindformatformat.listgetgetObjectSlotsgrepgreplimageintersectinvertStrandIQRis.unsortedlapplymadMapmapplymatchmeanmgetncolNCOLncolsnormalizenrowNROWnrowsOntologyorderorganismorganism<-pastepathpath<-plotDispEstsplotMAplotPCApmaxpmax.intpminpmin.intposPositionrankrbindReducerelistrep.intresidualsrownamesrownames<-sapplysaveRDSscorescore<-sdsetdiffsizeFactorssizeFactors<-sortspeciesspecies<-startstart<-strandstrand<-subsetttabletapplytoTabletypetype<-unionuniqueunlistunsplitunstrandupdateObjectupdateObjectFromSlotsvarweightswhichwhich.maxwhich.minwidthwidth<-xtabs

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
S4 generic functions for BioconductorBiocGenerics-package BiocGenerics
Accessing annotation informationannotation annotation<-
Transposing an array-like objectaperm
Append elements to a vector-like objectappend
Coerce to a data frameas.data.frame
Coerce to a listas.list
Coerce an object into a vectoras.vector
Box plotsboxplot
Combine objects by rows or columnscbind rbind
Combining or merging different Bioconductor data structurescombine combine,ANY,missing-method combine,data.frame,data.frame-method combine,matrix,matrix-method
Does an object contain out-of-memory data?class:OutOfMemoryObject containsOutOfMemoryData containsOutOfMemoryData,ANY-method containsOutOfMemoryData,environment-method containsOutOfMemoryData,list-method containsOutOfMemoryData,OutOfMemoryObject-method OutOfMemoryObject OutOfMemoryObject-class
Accessing SQLite DB informationdbconn dbfile
Kernel density estimationdensity
Accessors and generic functions used in the context of count datasetsconditions conditions<- counts counts<- design design<- dge dispTable dispTable<- estimateDispersions estimateSizeFactors plotDispEsts sizeFactors sizeFactors<-
Get the dimensions of each element of a list-like objectdims ncols nrows
Execute a function calldo.call
Determine duplicate elementsanyDuplicated duplicated
Evaluate an (unevaluated) expressioneval
Evaluate an (unevaluated) expressionevalq
Maxima and minimaExtremes pmax pmax.int pmin pmin.int
Accessing the file name of an objectfileName
Format an R object for pretty printingformat format.list
Common higher-order functions in functional programming languagesFilter Find funprog Map Position Reduce
Return the value of a named objectget mget
Pattern Matching and Replacementgrep grepl
Display a color imageimage
The Interquartile RangeIQR
Test if a vector-like object is not sortedis.unsorted
Apply a function over a list-like or vector-like objectlapply sapply
Median Absolute Deviationmad
Apply a function to multiple list-like or vector-like argumentsmapply
Value matching%in% match
Arithmetic Meanmean
Normalize an objectnormalize
The number of rows/columns of an array-like objectNCOL ncol NROW nrow
Generic Ontology getterOntology
Ordering permutationorder
Organism and species accessorsorganism organism<- organism_species species species<-
Concatenate stringspaste
Accessing the path of an objectbasename basename,ANY-method basename<- basename<-,ANY-method basename<-,character-method dirname dirname,ANY-method dirname<- dirname<-,ANY-method dirname<-,character-method path path<-
MA-plot: plot differences versus averages for high-throughput dataplotMA plotMA,ANY-method
PCA-plot: Principal Component Analysis plotplotPCA
Ranks the values in a vector-like objectrank
Re-listing an unlist()ed objectrelist
Replicate elements of a vector-like objectrep.int
Extract model residualsresiduals
Row and column namescolnames colnames<- row+colnames rownames rownames<-
S3 classes as S4 classesAsIs-class bzfile-class character_OR_connection-class connection-class dist-class fifo-class file-class gzcon-class gzfile-class pipe-class S3-classes-as-S4-classes sockconn-class terminal-class textConnection-class unz-class url-class
The saveRDS() S4 generic and default methodsaveRDS saveRDS,ANY-method
Score accessorscore score<-
Set operationsintersect setdiff sets union
Sorting a vector-like objectsort
The start(), end(), width(), and pos() generic getters and settersend end<- pos start start<- width width<-
Accessing strand informationinvertStrand invertStrand,ANY-method strand strand<- unstrand
Subsetting vector-like, matrix-like and data-frame-like objectssubset
Matrix Transposet
Cross tabulation and table creationtable
Apply a function over a ragged arraytapply
Run RUnit package unit teststestPackage
An alternative to as.data.frame()toTable
Accessing the type of an objecttype type,array-method type,data.frame-method type,factor-method type,vector-method type<- type<-,array-method type<-,vector-method
Extract unique elementsunique
Flatten list-like objectsunlist
Unsplit a list-like objectunsplit
Update an object to its current class definitiongetObjectSlots updateObject updateObject,ANY-method updateObject,environment-method updateObject,envRefClass-method updateObject,formula-method updateObject,list-method updateObjectFromSlots
Variance and Standard Deviationsd var
Extract model weightsweights
Which values in an object are considered TRUE?which
What's the index of the first min or max value in an object?which.max which.min
Cross tabulationxtabs