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.

### Usage

    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 2.0.2 Index]