ribo-class: Ribo Class

In ribosomeprofiling/ribor: An R Interface for Ribo Files

Description

The Ribo object serves as the main utility vehicle for the ribor package. Specifically, it allows the user to interface with a .ribo file in the R ribor rely on the Ribo object to read, visualize, and inspect the contents of the .ribo file. The information stored in this object include the .ribo file path, the list of experiments, the format version, the reference model, the minimum read length, maximum read length, the left span, the right span, and other transcript information.

Usage

## S4 method for signature 'Ribo'
show(object)

## S4 method for signature 'Ribo'
path(object)

## S4 method for signature 'Ribo'
experiments(object)

## S4 method for signature 'Ribo'
format_version(object)

## S4 method for signature 'Ribo'
reference(object)

## S4 method for signature 'Ribo'
length_min(object)

## S4 method for signature 'Ribo'
length_max(object)

## S4 method for signature 'Ribo'
left_span(object)

## S4 method for signature 'Ribo'
right_span(object)

## S4 method for signature 'Ribo'
metagene_radius(object)

## S4 method for signature 'Ribo'
length_offset(object)

## S4 method for signature 'Ribo'
has_metadata(object)

## S4 method for signature 'Ribo'
experiment_info(object)

## S4 method for signature 'Ribo'
transcript_info(object)

## S4 method for signature 'Ribo'
alias_hash(object)

## S4 method for signature 'Ribo'
original_hash(object)

Ribo(path, rename = NULL)

Arguments

object	Ribo object
path	The path to the .ribo file
rename	A function that renames the original transcript or an already generated character vector of aliases

Details

Note that the path parameter takes in a file path and stores it. While using the package, be sure to not to move or change the location of the .ribo file. The default names of the transcripts may be difficult to use depending on the settings used to generate the .ribo file. As a result, we have provided a rename parameter that integrates well with the Appris reference transcriptome. Users may also define a simple function that processes a given default transcript name in a one-to-one manner to another custom alias.

Value

Returns an S4 object of class "Ribo" containing a path to the HDF5 file, various attributes in the root folder, and information about the transcripts such as names and lengths

See Also

If a ribo object is already generated but aliases want to be added or updated, use the set_aliases function.

Examples

file.path <- system.file("extdata", "sample.ribo", package = "ribor")
sample <- Ribo(file.path)

show(sample)

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

ribosomeprofiling/ribor documentation built on May 21, 2021, 8:02 a.m.