set_aliases {ribor} | R Documentation

## Set the aliases of a ribo object

### Description

The function `set_aliases` allows the user to add aliases to a valid ribo object.

### Usage

    set_aliases(ribo.object, rename)

### Arguments

`ribo.object` | A 'ribo' object
`rename` | A function that renames original transcript name into an alias

### Details

If there is a different naming convention from the default appris transcriptome, there may be no simple way to generate convenient aliases from the original reference names. As a result, the user can first generate the ribo object and get the reference names, use custom (and likely more intricate) functions to generate a list of aliases, and then pass in a character vector of these aliases. The character vector should match the order of and correspond to the list of reference names retrieved from `get_reference_names`

### Value

A modified 'ribo' object that contains alias information

### Examples

    #generate a ribo object with transcript nicknames/aliases
    file.path <- system.file("extdata", "HEK293_ingolia.ribo", package = "ribor")
    sample <- Ribo(file.path)
    sample <- set_aliases(ribo.object = sample,
                          rename = rename_default)

[Package ribor version 0.99.8 Index]