CTSStoGenes {CAGEr} | R Documentation

## Make a gene expression table.

### Description

Add a gene expression table in the `GeneExpSE` experiment slot of an annotated `CAGEexp` object. `CAGEset` objects are not supported.

### Usage

    CTSStoGenes(object)

    ## S4 method for signature 'CAGEset'
    CTSStoGenes(object)

    ## S4 method for signature 'CAGEexp'
    CTSStoGenes(object)

### Arguments

`object` | A `CAGEexp` object that was annotated with the `annotateCTSS()` function.

### Value

The input object with the following modifications:

- A new `geneExpMatrix` experiment containing gene expression levels as a `SummarizedExperiment` object with one assay called `counts`, which is plain `matrix` of integers. (This plays better than `Rle DataFrames` when interfacing with downstream packages like DESeq2, and since the number of genes is limited, a `matrix` will not cause problems of performance.)

- New `genes` column data added, indicating total number of gene symbols detected per library.

- New `unannotated` column data added, indicating for each sample the number of counts that did not overlap with a known gene.

### Author(s)

Charles Plessy

### See Also

`annotateCTSS()`.

Other CAGEr object modifiers: `CustomConsensusClusters`, `aggregateTagClusters`, `annotateCTSS`, `clusterCTSS`, `cumulativeCTSSdistribution`, `getCTSS`, `normalizeTagCount`, `quantilePositions`, `summariseChrExpr`

Other CAGEr gene expression analysis functions: `GeneExpDESeq2`, `ranges2genes`

### Examples

    CTSStoGenes(exampleCAGEexp)
    all( librarySizes(exampleCAGEexp) -
         colSums(SummarizedExperiment::assay(GeneExpSE(exampleCAGEexp))) ==
         exampleCAGEexp$unannotated)

[Package CAGEr version 1.22.3 Index]