get_length_distribution {ribor} | R Documentation

## Retrieves the length distribution of a given region

### Description

The function `get_length_distribution` retrieves the raw or normalized counts at each read length from 'range.lower' to 'range.upper'.

### Usage

    get_length_distribution(
      ribo.object,
      region,
      range.lower = length_min(ribo.object),
      range.upper = length_max(ribo.object),
      compact = TRUE,
      experiment = experiments(ribo.object)
    )

### Arguments

`ribo.object` | A 'Ribo' object
`region` | Specific region of interest
`range.lower` | Lower bound of the read length, inclusive
`range.upper` | Upper bound of the read length, inclusive
`compact` | Option to return a DataFrame with Rle and factor as opposed to a raw data.frame
`experiment` | List of experiment names

### Details

This function is a wrapper function of `get_region_counts`, and the returned DataFrame is valid input for `plot_length_distribution`.

### Value

An annotated DataFrame or data.frame (if the compact parameter is set to FALSE) of the read-length specific region count information for a single region specified in the 'region' parameter. The returned data frame will have a length column, and it will not contain a transcript column.

### See Also

`plot_length_distribution` to plot the output of this function

### Examples

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

    #specify the experiments of interest
    experiments <- c("Hela_1", "Hela_2", "WT_1")

    #gets the normalized length distribution from read length 2 to 5
    length.dist <- get_length_distribution(ribo.object = sample,
                                           region = "CDS",
                                           range.lower = 2,
                                           range.upper = 5)

[Package ribor version 1.4.0 Index]