get_tidy_metagene {ribor} | R Documentation

## Retrieves the metagene data in a tidy format

### Description

The function `get_tidy_metagene` provides the user with a tidy data format for easier data cleaning and manipulation. In providing this functionality while reducing the returned data frame size, the user must aggregate across the transcripts and is only provided the option to aggregate the read lengths together.

### Usage

    get_tidy_metagene(
      ribo.object,
      site,
      range.lower = length_min(ribo.object),
      range.upper = length_max(ribo.object),
      length = TRUE,
      compact = TRUE,
      experiment = experiments(ribo.object)
    )

### Arguments

`ribo.object` | A 'Ribo' object
`site` | "start" or "stop" site coverage
`range.lower` | Lower bound of the read length, inclusive
`range.upper` | Upper bound of the read length, inclusive
`length` | Logical value that denotes if the metagene information should be summed across read lengths
`compact` | Option to return a DataFrame with Rle and factor as opposed to a raw data.frame
`experiment` | List of experiment names

### Details

The dimensions of the returned data frame depend on the parameters range.lower, range.upper, and length.

The param 'length' condenses the read lengths together. When length is TRUE, then the resulting data frame prints out one row for each experiment. This provides a tidy format of the metagene information across all transcripts and all read lengths in a given experiment. Each row in the data frame represents the total metagene coverage count of a given experiment at a given position.

When the param 'length' is FALSE, then the resulting data frame prints out the metagene coverage count at each position of the metagene radius for each read length. This provides a tidy format of the metagene information across the transcripts, preserving the metagene coverage count at each read length.

### Value

An annotated, tidy DataFrame or data.frame (if the compact parameter is set to FALSE) of the metagene information for either the 'stop' or 'start' site provided in the 'site' parameter. The data frame, as a result of its tidy property, will have a position column. The returned data frame will have a length column when the 'length' parameter is set to FALSE, indicating will be automatically aggregated to keep the memory footprint of this function reasonable.

### See Also

`Ribo` to generate the necessary 'Ribo' class object. `plot_metagene` to visualize the metagene data, `get_metagene` to obtain tidy metagene data under certain conditions

### Examples

    #generate the ribo object by loading in a ribo function and calling the \code{\link{Ribo}} function
    file.path <- system.file("extdata", "sample.ribo", package = "ribor")
    sample <- Ribo(file.path)

    #extract the total metagene information in a tidy format
    #for all experiments across the read lengths and transcripts
    #of the start site from read length 2 to 5

    metagene_info <- get_tidy_metagene(ribo.object = sample,
                                       site = "start",
                                       range.lower = 2,
                                       range.upper = 5,
                                       length = TRUE,
                                       experiment = experiments(sample))

    #Note that length and experiments in this case are the
    #default values and can be left out. The following generates the same output.
    metagene_info <- get_tidy_metagene(ribo.object = sample,
                                       site = "start",
                                       range.lower = 2,
                                       range.upper = 5)

[Package ribor version 1.4.0 Index]