ranges2genes {CAGEr} | R Documentation

## ranges2genes

### Description

Assign gene symbol(s) to Genomic Ranges.

### Usage

    ranges2genes(ranges, genes)

### Arguments

`ranges` | Genomics Ranges object, for example extracted from a RangedSummarizedExperiment object with the `rowRanges` command.
`genes` | A `GRanges` object containing `gene_name` metadata.

### Details

This private (non-exported) function is used to assign gene symbols to genomic ranges. It is run by `annotateCTSS`, which has to be run before `CTSStoGenes`.

### Value

A `Rle` character vector of same length as the GRanges object, indicating one gene symbol or a semicolon-separated list of gene symbols for each range.

### Author(s)

Charles Plessy

### See Also

`CTSScoordinatesGR`, `exampleZv9_annot`

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

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

### Examples

    CAGEr:::ranges2genes(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)

[Package CAGEr version 1.30.3 Index]