ranges2annot {CAGEr} | R Documentation

## hierarchical annotation of CTSSes

### Description

Assigns region types such as promoter, exon or unknown to CTSSes.

### Usage

    ranges2annot(ranges, annot)

### Arguments

`ranges` | The CTSS (GRanges) object, for example extracted from a RangedSummarizedExperiment object with the `rowRanges` command.
`annot` | A `GRanges` from which promoter positions will be inferred. Typically GENCODE. If the `type` metadata is present, it should contain ‘gene’, ‘exon’ and ‘transcript’ among its values. Otherwise, all entries are considered transcripts. If the `transcript_type` metadata is available, the entries may be not primary products (for instance ‘snoRNA’) are discarded.

### Details

Only the biotypes that are likely to have a promoter will be filtered in. This is currently hardcoded in the function; see its source code. Example of biotypes without a promoter: VDJ segments, etc.

### Value

A Run-length-encoded (Rle) factor of same length as the GRanges object, indicating if the interval is promoter, exon, intron or unknown, or just promoter, gene, unknown if the `type` metadata is absent.

### Author(s)

Charles Plessy

### See Also

`CTSScoordinatesGR`, `exampleZv9_annot`

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

### Examples

    CAGEr:::ranges2annot(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)

[Package CAGEr version 1.22.3 Index]