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<h1> S4 generic functions for Bioconductor
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</div><h2>Documentation for package ‘BiocGenerics’ version 0.16.0</h2>
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<table width="100%">
<tr><td style="width: 25%;"><a href="BiocGenerics-package.html">BiocGenerics-package</a></td>
<td>S4 generic functions for Bioconductor</td></tr>
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<h2><a name="A">-- A --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="annotation.html">annotation</a></td>
<td>Accessing annotation information</td></tr>
<tr><td style="width: 25%;"><a href="annotation.html">annotation<-</a></td>
<td>Accessing annotation information</td></tr>
<tr><td style="width: 25%;"><a href="duplicated.html">anyDuplicated</a></td>
<td>Determine duplicate elements</td></tr>
<tr><td style="width: 25%;"><a href="append.html">append</a></td>
<td>Append elements to a vector-like object</td></tr>
<tr><td style="width: 25%;"><a href="as.data.frame.html">as.data.frame</a></td>
<td>Coerce an object into a data frame</td></tr>
<tr><td style="width: 25%;"><a href="as.vector.html">as.vector</a></td>
<td>Coerce an object into a vector</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">AsIs-class</a></td>
<td>S3 classes as S4 classes</td></tr>
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<h2><a name="B">-- B --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="BiocGenerics-package.html">BiocGenerics</a></td>
<td>S4 generic functions for Bioconductor</td></tr>
<tr><td style="width: 25%;"><a href="boxplot.html">boxplot</a></td>
<td>Box plots</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">bzfile-class</a></td>
<td>S3 classes as S4 classes</td></tr>
</table>
<h2><a name="C">-- C --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="cbind.html">cbind</a></td>
<td>Combine objects by rows or columns</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">characterORconnection-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterApply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterApplyLB</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterCall</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterEvalQ</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterExport</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterMap</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">clusterSplit</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="row_colnames.html">colnames</a></td>
<td>Row and column names</td></tr>
<tr><td style="width: 25%;"><a href="row_colnames.html">colnames<-</a></td>
<td>Row and column names</td></tr>
<tr><td style="width: 25%;"><a href="combine.html">combine</a></td>
<td>Combining or merging different Bioconductor data structures</td></tr>
<tr><td style="width: 25%;"><a href="combine.html">combine-method</a></td>
<td>Combining or merging different Bioconductor data structures</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">conditions</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">conditions<-</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">connection-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">counts</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">counts<-</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
</table>
<h2><a name="D">-- D --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="dbconn.html">dbconn</a></td>
<td>Accessing SQLite DB information</td></tr>
<tr><td style="width: 25%;"><a href="dbconn.html">dbfile</a></td>
<td>Accessing SQLite DB information</td></tr>
<tr><td style="width: 25%;"><a href="density.html">density</a></td>
<td>Kernel density estimation</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">design</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">design<-</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">dispTable</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">dispTable<-</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">dist-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="do.call.html">do.call</a></td>
<td>Execute a function call</td></tr>
<tr><td style="width: 25%;"><a href="duplicated.html">duplicated</a></td>
<td>Determine duplicate elements</td></tr>
</table>
<h2><a name="E">-- E --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="start.html">end</a></td>
<td>Start, end, width generic getters and setters</td></tr>
<tr><td style="width: 25%;"><a href="start.html">end<-</a></td>
<td>Start, end, width generic getters and setters</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">estimateDispersions</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">estimateSizeFactors</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="eval.html">eval</a></td>
<td>Evaluate an (unevaluated) expression</td></tr>
<tr><td style="width: 25%;"><a href="evalq.html">evalq</a></td>
<td>Evaluate an (unevaluated) expression</td></tr>
<tr><td style="width: 25%;"><a href="Extremes.html">Extremes</a></td>
<td>Maxima and minima</td></tr>
</table>
<h2><a name="F">-- F --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">fifo-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">file-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="fileName.html">fileName</a></td>
<td>Accessing the file name of an object</td></tr>
<tr><td style="width: 25%;"><a href="funprog.html">Filter</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td style="width: 25%;"><a href="funprog.html">Find</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td style="width: 25%;"><a href="funprog.html">funprog</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
</table>
<h2><a name="G">-- G --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="get.html">get</a></td>
<td>Return the value of a named object</td></tr>
<tr><td style="width: 25%;"><a href="updateObject.html">getObjectSlots</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td style="width: 25%;"><a href="grep.html">grep</a></td>
<td>Pattern Matching and Replacement</td></tr>
<tr><td style="width: 25%;"><a href="grep.html">grepl</a></td>
<td>Pattern Matching and Replacement</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">gzcon-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">gzfile-class</a></td>
<td>S3 classes as S4 classes</td></tr>
</table>
<h2><a name="I">-- I --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="image.html">image</a></td>
<td>Display a color image</td></tr>
<tr><td style="width: 25%;"><a href="sets.html">intersect</a></td>
<td>Set operations</td></tr>
<tr><td style="width: 25%;"><a href="IQR.html">IQR</a></td>
<td>The Interquartile Range</td></tr>
<tr><td style="width: 25%;"><a href="is.unsorted.html">is.unsorted</a></td>
<td>Test if a vector-like object is not sorted</td></tr>
</table>
<h2><a name="L">-- L --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="lapply.html">lapply</a></td>
<td>Apply a function over a list-like or vector-like object</td></tr>
<tr><td style="width: 25%;"><a href="lengths.html">lengths</a></td>
<td>Lengths of the list elements of a list-like object</td></tr>
</table>
<h2><a name="M">-- M --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="mad.html">mad</a></td>
<td>Median Absolute Deviation</td></tr>
<tr><td style="width: 25%;"><a href="funprog.html">Map</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td style="width: 25%;"><a href="mapply.html">mapply</a></td>
<td>Apply a function to multiple list-like or vector-like arguments</td></tr>
<tr><td style="width: 25%;"><a href="match.html">match</a></td>
<td>Value matching</td></tr>
<tr><td style="width: 25%;"><a href="get.html">mget</a></td>
<td>Return the value of a named object</td></tr>
</table>
<h2><a name="N">-- N --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="nrow.html">NCOL</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
<tr><td style="width: 25%;"><a href="nrow.html">ncol</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
<tr><td style="width: 25%;"><a href="normalize.html">normalize</a></td>
<td>Normalize an object</td></tr>
<tr><td style="width: 25%;"><a href="nrow.html">NROW</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
<tr><td style="width: 25%;"><a href="nrow.html">nrow</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
</table>
<h2><a name="O">-- O --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="order.html">order</a></td>
<td>Ordering permutation</td></tr>
<tr><td style="width: 25%;"><a href="organism_species.html">organism</a></td>
<td>Organism and species accessors</td></tr>
<tr><td style="width: 25%;"><a href="organism_species.html">organism<-</a></td>
<td>Organism and species accessors</td></tr>
<tr><td style="width: 25%;"><a href="organism_species.html">organism_species</a></td>
<td>Organism and species accessors</td></tr>
</table>
<h2><a name="P">-- P --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="clusterApply.html">parApply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">parCapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">parLapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">parLapplyLB</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">parRapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">parSapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="clusterApply.html">parSapplyLB</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td style="width: 25%;"><a href="paste.html">paste</a></td>
<td>Concatenate strings</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">pipe-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">plotDispEsts</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="plotMA.html">plotMA</a></td>
<td>MA-plot: plot differences versus averages for high-throughput data</td></tr>
<tr><td style="width: 25%;"><a href="plotMA.html">plotMA-method</a></td>
<td>MA-plot: plot differences versus averages for high-throughput data</td></tr>
<tr><td style="width: 25%;"><a href="plotPCA.html">plotPCA</a></td>
<td>PCA-plot: Principal Component Analysis plot</td></tr>
<tr><td style="width: 25%;"><a href="plotPCA.html">plotPCA-method</a></td>
<td>PCA-plot: Principal Component Analysis plot</td></tr>
<tr><td style="width: 25%;"><a href="Extremes.html">pmax</a></td>
<td>Maxima and minima</td></tr>
<tr><td style="width: 25%;"><a href="Extremes.html">pmax.int</a></td>
<td>Maxima and minima</td></tr>
<tr><td style="width: 25%;"><a href="Extremes.html">pmin</a></td>
<td>Maxima and minima</td></tr>
<tr><td style="width: 25%;"><a href="Extremes.html">pmin.int</a></td>
<td>Maxima and minima</td></tr>
<tr><td style="width: 25%;"><a href="funprog.html">Position</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
</table>
<h2><a name="R">-- R --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="rank.html">rank</a></td>
<td>Ranks the values in a vector-like object</td></tr>
<tr><td style="width: 25%;"><a href="cbind.html">rbind</a></td>
<td>Combine objects by rows or columns</td></tr>
<tr><td style="width: 25%;"><a href="funprog.html">Reduce</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td style="width: 25%;"><a href="relist.html">relist</a></td>
<td>Re-listing an unlist()ed object</td></tr>
<tr><td style="width: 25%;"><a href="rep.html">rep.int</a></td>
<td>Replicate elements of a vector-like object</td></tr>
<tr><td style="width: 25%;"><a href="residuals.html">residuals</a></td>
<td>Extract model residuals</td></tr>
<tr><td style="width: 25%;"><a href="row_colnames.html">row+colnames</a></td>
<td>Row and column names</td></tr>
<tr><td style="width: 25%;"><a href="row_colnames.html">rownames</a></td>
<td>Row and column names</td></tr>
<tr><td style="width: 25%;"><a href="row_colnames.html">rownames<-</a></td>
<td>Row and column names</td></tr>
</table>
<h2><a name="S">-- S --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">S3-classes-as-S4-classes</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="lapply.html">sapply</a></td>
<td>Apply a function over a list-like or vector-like object</td></tr>
<tr><td style="width: 25%;"><a href="score.html">score</a></td>
<td>Score accessor</td></tr>
<tr><td style="width: 25%;"><a href="score.html">score<-</a></td>
<td>Score accessor</td></tr>
<tr><td style="width: 25%;"><a href="sets.html">setdiff</a></td>
<td>Set operations</td></tr>
<tr><td style="width: 25%;"><a href="sets.html">sets</a></td>
<td>Set operations</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">sizeFactors</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="dge.html">sizeFactors<-</a></td>
<td>Accessors and generic functions used in the context of count datasets</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">sockconn-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="sort.html">sort</a></td>
<td>Sorting a vector-like object</td></tr>
<tr><td style="width: 25%;"><a href="organism_species.html">species</a></td>
<td>Organism and species accessors</td></tr>
<tr><td style="width: 25%;"><a href="organism_species.html">species<-</a></td>
<td>Organism and species accessors</td></tr>
<tr><td style="width: 25%;"><a href="start.html">start</a></td>
<td>Start, end, width generic getters and setters</td></tr>
<tr><td style="width: 25%;"><a href="start.html">start<-</a></td>
<td>Start, end, width generic getters and setters</td></tr>
<tr><td style="width: 25%;"><a href="strand.html">strand</a></td>
<td>Accessing strand information</td></tr>
<tr><td style="width: 25%;"><a href="strand.html">strand<-</a></td>
<td>Accessing strand information</td></tr>
<tr><td style="width: 25%;"><a href="subset.html">subset</a></td>
<td>Subsetting vector-like, matrix-like and data-frame-like objects</td></tr>
</table>
<h2><a name="T">-- T --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="table.html">table</a></td>
<td>Cross tabulation and table creation</td></tr>
<tr><td style="width: 25%;"><a href="tapply.html">tapply</a></td>
<td>Apply a function over a ragged array</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">terminal-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="testPackage.html">testPackage</a></td>
<td>Run RUnit package unit tests</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">textConnection-class</a></td>
<td>S3 classes as S4 classes</td></tr>
</table>
<h2><a name="U">-- U --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="sets.html">union</a></td>
<td>Set operations</td></tr>
<tr><td style="width: 25%;"><a href="unique.html">unique</a></td>
<td>Extract unique elements</td></tr>
<tr><td style="width: 25%;"><a href="unlist.html">unlist</a></td>
<td>Flatten list-like objects</td></tr>
<tr><td style="width: 25%;"><a href="unsplit.html">unsplit</a></td>
<td>Unsplit a list-like object</td></tr>
<tr><td style="width: 25%;"><a href="strand.html">unstrand</a></td>
<td>Accessing strand information</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">unz-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td style="width: 25%;"><a href="updateObject.html">updateObject</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td style="width: 25%;"><a href="updateObject.html">updateObject-method</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td style="width: 25%;"><a href="updateObject.html">updateObjectFromSlots</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td style="width: 25%;"><a href="S3-classes-as-S4-classes.html">url-class</a></td>
<td>S3 classes as S4 classes</td></tr>
</table>
<h2><a name="W">-- W --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="weights.html">weights</a></td>
<td>Extract model weights</td></tr>
<tr><td style="width: 25%;"><a href="start.html">width</a></td>
<td>Start, end, width generic getters and setters</td></tr>
<tr><td style="width: 25%;"><a href="start.html">width<-</a></td>
<td>Start, end, width generic getters and setters</td></tr>
</table>
<h2><a name="X">-- X --</a></h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="xtabs.html">xtabs</a></td>
<td>Cross tabulation</td></tr>
</table>
</body></html>
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