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<html><head><title>R: Generic functions for Bioconductor</title>
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<h1> Generic functions for Bioconductor
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</div><h2>Documentation for package ‘BiocGenerics’ version 0.8.0</h2>
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<tr><td width="25%"><a href="BiocGenerics-package.html">BiocGenerics-package</a></td>
<td>Generic functions for Bioconductor</td></tr>
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<h2><a name="A">-- A --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="annotation.html">annotation</a></td>
<td>Accessing annotation information</td></tr>
<tr><td width="25%"><a href="annotation.html">annotation<-</a></td>
<td>Accessing annotation information</td></tr>
<tr><td width="25%"><a href="duplicated.html">anyDuplicated</a></td>
<td>Determine duplicate elements</td></tr>
<tr><td width="25%"><a href="append.html">append</a></td>
<td>Append elements to a vector-like object</td></tr>
<tr><td 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 width="25%"><a href="as.vector.html">as.vector</a></td>
<td>Coerce an object into a vector</td></tr>
<tr><td 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>
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<tr><td width="25%"><a href="BiocGenerics-package.html">BiocGenerics</a></td>
<td>Generic functions for Bioconductor</td></tr>
<tr><td width="25%"><a href="boxplot.html">boxplot</a></td>
<td>Box plots</td></tr>
<tr><td 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 width="25%"><a href="cbind.html">cbind</a></td>
<td>Combine objects by rows or columns</td></tr>
<tr><td width="25%"><a href="S3-classes-as-S4-classes.html">characterORconnection-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterApply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterApplyLB</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterCall</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterEvalQ</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterExport</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterMap</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">clusterSplit</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="row_colnames.html">colnames</a></td>
<td>Row and column names</td></tr>
<tr><td width="25%"><a href="combine.html">combine</a></td>
<td>Combining or merging different Bioconductor data structures</td></tr>
<tr><td width="25%"><a href="combine.html">combine-method</a></td>
<td>Combining or merging different Bioconductor data structures</td></tr>
<tr><td 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 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 width="25%"><a href="S3-classes-as-S4-classes.html">connection-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td 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 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 width="25%"><a href="density.html">density</a></td>
<td>Kernel density estimation</td></tr>
<tr><td 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 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 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 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 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 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 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 width="25%"><a href="eval.html">eval</a></td>
<td>Evaluate an (unevaluated) expression</td></tr>
<tr><td width="25%"><a href="evalq.html">evalq</a></td>
<td>Evaluate an (unevaluated) expression</td></tr>
<tr><td 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 width="25%"><a href="S3-classes-as-S4-classes.html">fifo-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td width="25%"><a href="S3-classes-as-S4-classes.html">file-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td width="25%"><a href="funprog.html">Filter</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td width="25%"><a href="funprog.html">Find</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td 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 width="25%"><a href="get.html">get</a></td>
<td>Return the value of a named object</td></tr>
<tr><td width="25%"><a href="updateObject.html">getObjectSlots</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td width="25%"><a href="S3-classes-as-S4-classes.html">gzcon-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td 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 width="25%"><a href="image.html">image</a></td>
<td>Display a color image</td></tr>
<tr><td width="25%"><a href="sets.html">intersect</a></td>
<td>Set operations</td></tr>
<tr><td width="25%"><a href="is.unsorted.html">is.unsorted</a></td>
<td>Test if an Object is Not Sorted</td></tr>
</table>
<h2><a name="L">-- L --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="lapply.html">lapply</a></td>
<td>Apply a function over a list-like or vector-like object</td></tr>
</table>
<h2><a name="M">-- M --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="funprog.html">Map</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td 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 width="25%"><a href="match.html">match</a></td>
<td>Value matching</td></tr>
<tr><td 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 width="25%"><a href="nrow.html">NCOL</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
<tr><td width="25%"><a href="nrow.html">ncol</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
<tr><td width="25%"><a href="normalize.html">normalize</a></td>
<td>Normalize an object</td></tr>
<tr><td width="25%"><a href="nrow.html">NROW</a></td>
<td>The number of rows/columns of an array-like object</td></tr>
<tr><td 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 width="25%"><a href="order.html">order</a></td>
<td>Ordering permutation</td></tr>
</table>
<h2><a name="P">-- P --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="clusterApply.html">parApply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">parCapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">parLapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">parLapplyLB</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">parRapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">parSapply</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="clusterApply.html">parSapplyLB</a></td>
<td>Apply operations using clusters</td></tr>
<tr><td width="25%"><a href="paste.html">paste</a></td>
<td>Concatenate strings</td></tr>
<tr><td width="25%"><a href="S3-classes-as-S4-classes.html">pipe-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td 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 width="25%"><a href="plotMA.html">plotMA</a></td>
<td>MA-plot: plot differences versus averages for high-throughput data</td></tr>
<tr><td 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 width="25%"><a href="Extremes.html">pmax</a></td>
<td>Maxima and minima</td></tr>
<tr><td width="25%"><a href="Extremes.html">pmax.int</a></td>
<td>Maxima and minima</td></tr>
<tr><td width="25%"><a href="Extremes.html">pmin</a></td>
<td>Maxima and minima</td></tr>
<tr><td width="25%"><a href="Extremes.html">pmin.int</a></td>
<td>Maxima and minima</td></tr>
<tr><td 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 width="25%"><a href="rank.html">rank</a></td>
<td>Ranks the values in a vector-like object</td></tr>
<tr><td width="25%"><a href="cbind.html">rbind</a></td>
<td>Combine objects by rows or columns</td></tr>
<tr><td width="25%"><a href="funprog.html">Reduce</a></td>
<td>Common higher-order functions in functional programming languages</td></tr>
<tr><td width="25%"><a href="rep.html">rep.int</a></td>
<td>Replicate elements of a vector-like object</td></tr>
<tr><td width="25%"><a href="residuals.html">residuals</a></td>
<td>Extract model residuals</td></tr>
<tr><td width="25%"><a href="row_colnames.html">row+colnames</a></td>
<td>Row and column names</td></tr>
<tr><td 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 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 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 width="25%"><a href="sets.html">setdiff</a></td>
<td>Set operations</td></tr>
<tr><td width="25%"><a href="sets.html">sets</a></td>
<td>Set operations</td></tr>
<tr><td 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 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 width="25%"><a href="S3-classes-as-S4-classes.html">sockconn-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td width="25%"><a href="sort.html">sort</a></td>
<td>Sorting a vector-like object</td></tr>
<tr><td width="25%"><a href="strand.html">strand</a></td>
<td>Accessing strand information</td></tr>
<tr><td width="25%"><a href="strand.html">strand<-</a></td>
<td>Accessing strand information</td></tr>
</table>
<h2><a name="T">-- T --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="table.html">table</a></td>
<td>Cross tabulation and table creation</td></tr>
<tr><td width="25%"><a href="tapply.html">tapply</a></td>
<td>Apply a function over a ragged array</td></tr>
<tr><td width="25%"><a href="S3-classes-as-S4-classes.html">terminal-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td 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 width="25%"><a href="sets.html">union</a></td>
<td>Set operations</td></tr>
<tr><td width="25%"><a href="unique.html">unique</a></td>
<td>Extract unique elements</td></tr>
<tr><td width="25%"><a href="unlist.html">unlist</a></td>
<td>Flatten list-like objects</td></tr>
<tr><td width="25%"><a href="S3-classes-as-S4-classes.html">unz-class</a></td>
<td>S3 classes as S4 classes</td></tr>
<tr><td width="25%"><a href="updateObject.html">updateObject</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td width="25%"><a href="updateObject.html">updateObject-method</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td width="25%"><a href="updateObject.html">updateObjectFromSlots</a></td>
<td>Update an object to its current class definition</td></tr>
<tr><td 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 width="25%"><a href="weights.html">weights</a></td>
<td>Extract model weights</td></tr>
</table>
<h2><a name="X">-- X --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="xtabs.html">xtabs</a></td>
<td>Cross tabulation</td></tr>
</table>
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