annotateCTSS {CAGEr} | R Documentation

## Annotate and compute summary statistics

### Description

`annotateCTSS` annotates the CTSS of a `CAGEexp` object and computes annotation statistics.

`annotateConsensusClusters` annotates the consensus clusters of a CAGEr object.

### Usage

    annotateCTSS(object, ranges)

    ## S4 method for signature 'CAGEset,ANY'
    annotateCTSS(object, ranges)

    ## S4 method for signature 'CAGEexp,GRanges'
    annotateCTSS(object, ranges)

    annotateConsensusClusters(object, ranges)

    ## S4 method for signature 'CAGEset,ANY'
    annotateConsensusClusters(object, ranges)

    ## S4 method for signature 'CAGEexp,GRanges'
    annotateConsensusClusters(object, ranges)

### Arguments

`object` | `CAGEexp` object (`CAGEset`s are not supported).
`ranges` | A `GRanges` object, optionally containing `gene_name`, `type` and `transcript_type` metadata.

### Value

`annotateCTSS` returns the input object with the following modifications:

- The Genomic Ranges of the `tagCountMatrix` experiment gains an `annotation` metadata column, with levels such as `promoter`, `exon`, `intron` and `unknown`. If the annotation has a `gene_name` metadata, then a `genes` column is also added, with gene symbols from the annotation.

- The sample metadata gets new columns, indicating total counts in each of the annotation levels. If the annotation has a `gene_name` metadata, then a `genes` column is added to indicate the number of different gene symbols detected.

`annotateConsensusClusters` returns the input object with the same modifications as above.

### Author(s)

Charles Plessy

### See Also

`CTSStoGenes`, and the `exampleZv9_annot` example data.

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

Other CAGEr annotation functions: `plotAnnot`, `ranges2annot`, `ranges2genes`, `ranges2names`

### Examples

    library(SummarizedExperiment)
    annotateCTSS(exampleCAGEexp, exampleZv9_annot)
    colData(exampleCAGEexp)

    annotateConsensusClusters(exampleCAGEexp, exampleZv9_annot)
    consensusClustersGR(exampleCAGEexp)

[Package CAGEr version 1.24.0 Index]