A B C D E F G I L M N O P R S T U V W X misc
| BiocGenerics-package | S4 generic functions for Bioconductor |
| add_prefix | Concatenate strings (binary form) |
| add_suffix | Concatenate strings (binary form) |
| annotation | Accessing annotation information |
| annotation<- | Accessing annotation information |
| anyDuplicated | Determine duplicate elements |
| aperm | Transposing an array-like object |
| append | Append elements to a vector-like object |
| as.data.frame | Coerce to a data frame |
| as.list | Coerce to a list |
| as.vector | Coerce an object into a vector |
| AsIs-class | S3 classes as S4 classes |
| basename | Accessing the path of an object |
| basename-method | Accessing the path of an object |
| basename<- | Accessing the path of an object |
| basename<--method | Accessing the path of an object |
| BiocGenerics | S4 generic functions for Bioconductor |
| boxplot | Box plots |
| bzfile-class | S3 classes as S4 classes |
| cbind | Combine objects by rows or columns |
| character_OR_connection-class | S3 classes as S4 classes |
| class:OutOfMemoryObject | Does an object contain out-of-memory data? |
| colnames | Row and column names |
| colnames<- | Row and column names |
| combine | Combining or merging different Bioconductor data structures |
| combine-method | Combining or merging different Bioconductor data structures |
| conditions | Accessors and generic functions used in the context of count datasets |
| conditions<- | Accessors and generic functions used in the context of count datasets |
| connection-class | S3 classes as S4 classes |
| containsOutOfMemoryData | Does an object contain out-of-memory data? |
| containsOutOfMemoryData-method | Does an object contain out-of-memory data? |
| counts | Accessors and generic functions used in the context of count datasets |
| counts<- | Accessors and generic functions used in the context of count datasets |
| dbconn | Accessing SQLite DB information |
| dbfile | Accessing SQLite DB information |
| density | Kernel density estimation |
| design | Accessors and generic functions used in the context of count datasets |
| design<- | Accessors and generic functions used in the context of count datasets |
| dge | Accessors and generic functions used in the context of count datasets |
| dims | Get the dimensions of each element of a list-like object |
| dirname | Accessing the path of an object |
| dirname-method | Accessing the path of an object |
| dirname<- | Accessing the path of an object |
| dirname<--method | Accessing the path of an object |
| dispTable | Accessors and generic functions used in the context of count datasets |
| dispTable<- | Accessors and generic functions used in the context of count datasets |
| dist-class | S3 classes as S4 classes |
| do.call | Execute a function call |
| duplicated | Determine duplicate elements |
| end | The start(), end(), width(), and pos() generic getters and setters |
| end<- | The start(), end(), width(), and pos() generic getters and setters |
| estimateDispersions | Accessors and generic functions used in the context of count datasets |
| estimateSizeFactors | Accessors and generic functions used in the context of count datasets |
| eval | Evaluate an (unevaluated) expression |
| evalq | Evaluate an (unevaluated) expression |
| Extremes | Maxima and minima |
| fifo-class | S3 classes as S4 classes |
| file-class | S3 classes as S4 classes |
| fileName | Accessing the file name of an object |
| Filter | Common higher-order functions in functional programming languages |
| Find | Common higher-order functions in functional programming languages |
| format | Format an R object for pretty printing |
| format.list | Format an R object for pretty printing |
| funprog | Common higher-order functions in functional programming languages |
| get | Return the value of a named object |
| getObjectSlots | Update an object to its current class definition |
| grep | Pattern Matching and Replacement |
| grepl | Pattern Matching and Replacement |
| gzcon-class | S3 classes as S4 classes |
| gzfile-class | S3 classes as S4 classes |
| image | Display a color image |
| intersect | Set operations |
| invertStrand | Accessing strand information |
| invertStrand-method | Accessing strand information |
| IQR | The Interquartile Range |
| is.unsorted | Test if a vector-like object is not sorted |
| lapply | Apply a function over a list-like or vector-like object |
| longForm | Turn object into long form |
| mad | Median Absolute Deviation |
| Map | Common higher-order functions in functional programming languages |
| mapply | Apply a function to multiple list-like or vector-like arguments |
| match | Value matching |
| mean | Arithmetic Mean |
| mget | Return the value of a named object |
| NCOL | The number of rows/columns of an array-like object |
| ncol | The number of rows/columns of an array-like object |
| ncols | Get the dimensions of each element of a list-like object |
| normalize | Normalize an object |
| NROW | The number of rows/columns of an array-like object |
| nrow | The number of rows/columns of an array-like object |
| nrows | Get the dimensions of each element of a list-like object |
| Ontology | Generic Ontology getter |
| order | Ordering permutation |
| organism | Organism and species accessors |
| organism<- | Organism and species accessors |
| organism_species | Organism and species accessors |
| OutOfMemoryObject | Does an object contain out-of-memory data? |
| OutOfMemoryObject-class | Does an object contain out-of-memory data? |
| paste | Concatenate strings |
| paste2 | Concatenate strings (binary form) |
| paste2-method | Concatenate strings (binary form) |
| path | Accessing the path of an object |
| path<- | Accessing the path of an object |
| pipe-class | S3 classes as S4 classes |
| plotDispEsts | Accessors and generic functions used in the context of count datasets |
| plotMA | MA-plot: plot differences versus averages for high-throughput data |
| plotMA-method | MA-plot: plot differences versus averages for high-throughput data |
| plotPCA | PCA-plot: Principal Component Analysis plot |
| pmax | Maxima and minima |
| pmax.int | Maxima and minima |
| pmin | Maxima and minima |
| pmin.int | Maxima and minima |
| pos | The start(), end(), width(), and pos() generic getters and setters |
| Position | Common higher-order functions in functional programming languages |
| rank | Ranks the values in a vector-like object |
| rbind | Combine objects by rows or columns |
| Reduce | Common higher-order functions in functional programming languages |
| relist | Re-listing an unlist()ed object |
| rep.int | Replicate elements of a vector-like object |
| residuals | Extract model residuals |
| row+colnames | Row and column names |
| rownames | Row and column names |
| rownames<- | Row and column names |
| S3-classes-as-S4-classes | S3 classes as S4 classes |
| sapply | Apply a function over a list-like or vector-like object |
| saveRDS | The saveRDS() S4 generic and default method |
| saveRDS-method | The saveRDS() S4 generic and default method |
| score | Score accessor |
| score<- | Score accessor |
| sd | Variance and Standard Deviation |
| setdiff | Set operations |
| setequal | Set operations |
| setops | Set operations |
| sets | Set operations |
| sizeFactors | Accessors and generic functions used in the context of count datasets |
| sizeFactors<- | Accessors and generic functions used in the context of count datasets |
| sockconn-class | S3 classes as S4 classes |
| sort | Sorting a vector-like object |
| species | Organism and species accessors |
| species<- | Organism and species accessors |
| start | The start(), end(), width(), and pos() generic getters and setters |
| start<- | The start(), end(), width(), and pos() generic getters and setters |
| strand | Accessing strand information |
| strand<- | Accessing strand information |
| subset | Subsetting vector-like, matrix-like and data-frame-like objects |
| t | Matrix Transpose |
| table | Cross tabulation and table creation |
| tapply | Apply a function over a ragged array |
| terminal-class | S3 classes as S4 classes |
| testPackage | Run RUnit package unit tests |
| textConnection-class | S3 classes as S4 classes |
| toTable | An alternative to as.data.frame() |
| type | Accessing the type of an object |
| type-method | Accessing the type of an object |
| type<- | Accessing the type of an object |
| type<--method | Accessing the type of an object |
| union | Set operations |
| unique | Extract unique elements |
| unlist | Flatten list-like objects |
| unsplit | Unsplit a list-like object |
| unstrand | Accessing strand information |
| unz-class | S3 classes as S4 classes |
| updateObject | Update an object to its current class definition |
| updateObject-method | Update an object to its current class definition |
| updateObjectFromSlots | Update an object to its current class definition |
| url-class | S3 classes as S4 classes |
| var | Variance and Standard Deviation |
| weights | Extract model weights |
| which | Which values in an object are considered TRUE? |
| which.max | What's the index of the first min or max value in an object? |
| which.min | What's the index of the first min or max value in an object? |
| width | The start(), end(), width(), and pos() generic getters and setters |
| width<- | The start(), end(), width(), and pos() generic getters and setters |
| xtabs | Cross tabulation |
| %in% | Value matching |