| S4 generic functions for Bioconductor | BiocGenerics-package BiocGenerics |
| Accessing annotation information | annotation annotation<- |
| Transposing an array-like object | aperm |
| Append elements to a vector-like object | append |
| Coerce to a data frame | as.data.frame |
| Coerce to a list | as.list |
| Coerce an object into a vector | as.vector |
| Box plots | boxplot |
| Combine objects by rows or columns | cbind rbind |
| Combining or merging different Bioconductor data structures | combine 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 information | dbconn dbfile |
| Kernel density estimation | density |
| Accessors and generic functions used in the context of count datasets | conditions conditions<- counts counts<- design design<- dge dispTable dispTable<- estimateDispersions estimateSizeFactors plotDispEsts sizeFactors sizeFactors<- |
| Get the dimensions of each element of a list-like object | dims ncols nrows |
| Execute a function call | do.call |
| Determine duplicate elements | anyDuplicated duplicated |
| Evaluate an (unevaluated) expression | eval |
| Evaluate an (unevaluated) expression | evalq |
| Maxima and minima | Extremes pmax pmax.int pmin pmin.int |
| Accessing the file name of an object | fileName |
| Format an R object for pretty printing | format format.list |
| Common higher-order functions in functional programming languages | Filter Find funprog Map Position Reduce |
| Return the value of a named object | get mget |
| Pattern Matching and Replacement | grep grepl |
| Display a color image | image |
| The Interquartile Range | IQR |
| Test if a vector-like object is not sorted | is.unsorted |
| Apply a function over a list-like or vector-like object | lapply sapply |
| Median Absolute Deviation | mad |
| Apply a function to multiple list-like or vector-like arguments | mapply |
| Value matching | %in% match |
| Arithmetic Mean | mean |
| Normalize an object | normalize |
| The number of rows/columns of an array-like object | NCOL ncol NROW nrow |
| Generic Ontology getter | Ontology |
| Ordering permutation | order |
| Organism and species accessors | organism organism<- organism_species species species<- |
| Concatenate strings | paste |
| Accessing the path of an object | basename 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 data | plotMA plotMA,ANY-method |
| PCA-plot: Principal Component Analysis plot | plotPCA |
| Ranks the values in a vector-like object | rank |
| Re-listing an unlist()ed object | relist |
| Replicate elements of a vector-like object | rep.int |
| Extract model residuals | residuals |
| Row and column names | colnames colnames<- row+colnames rownames rownames<- |
| S3 classes as S4 classes | AsIs-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 method | saveRDS saveRDS,ANY-method |
| Score accessor | score score<- |
| Set operations | intersect setdiff sets union |
| Sorting a vector-like object | sort |
| The start(), end(), width(), and pos() generic getters and setters | end end<- pos start start<- width width<- |
| Accessing strand information | invertStrand invertStrand,ANY-method strand strand<- unstrand |
| Subsetting vector-like, matrix-like and data-frame-like objects | subset |
| Matrix Transpose | t |
| Cross tabulation and table creation | table |
| Apply a function over a ragged array | tapply |
| Run RUnit package unit tests | testPackage |
| An alternative to as.data.frame() | toTable |
| Accessing the type of an object | type type,array-method type,data.frame-method type,factor-method type,vector-method type<- type<-,array-method type<-,vector-method |
| Extract unique elements | unique |
| Flatten list-like objects | unlist |
| Unsplit a list-like object | unsplit |
| Update an object to its current class definition | getObjectSlots updateObject updateObject,ANY-method updateObject,environment-method updateObject,envRefClass-method updateObject,formula-method updateObject,list-method updateObjectFromSlots |
| Variance and Standard Deviation | sd var |
| Extract model weights | weights |
| 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 tabulation | xtabs |
