get_coverage: Retrieves the coverage data for a given transcript
In ribosomeprofiling/ribor: An R Interface for Ribo Files

Description Usage Arguments Details Value See Also Examples

The function get_coverage generates a DataFrame of coverage data over the length of a given transcript.

get_coverage(
  ribo.object,
  name,
  range.lower = length_min(ribo.object),
  range.upper = length_max(ribo.object),
  length = TRUE,
  tidy = FALSE,
  alias = FALSE,
  compact = TRUE,
  experiment = experiments(ribo.object)
)

`ribo.object`	A 'Ribo' object
`name`	Transcript Name
`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 coverage should be summed across read lengths
`tidy`	Logical value denoting whether or not the user wants a tidy format
`alias`	Option to accept the transcript input as aliases/nicknames
`compact`	Option to return a DataFrame with Rle and factor as opposed to a raw data.frame
`experiment`	List of experiments to obtain coverage information on

The function get_coverage first checks the experiments in the 'experiments' parameter to see if they are present in the .ribo file. It will then check these experiments for coverage data which is an optional dataset. As a result, this function safe guards against experiments that do not have coverage data, but it also, by default, includes all of the experiments in a file in the experiments' parameter.

The function checks the coverage of one transcript at a time at each read length from 'range.lower' to 'range.upper', inclusive. However, the parameter 'length' allows the user to obtain the coverage information of a transcript across the range of read lengths indicated by 'range.lower' and 'range.upper'.

If the ribo.object is generated with aliases, the 'alias' parameter, if set to TRUE, allows the user to use the alias of the transcript as the 'name' parameter instead of the original transcript name.

An annotated DataFrame or data.frame (if the compact parameter is set to FALSE) of the coverage information for the provided list of 'experiments' in the 'experiment' parameter. The returned object will have a length column when the 'length' parameter is set to FALSE, indicating that the user does not want to sum the count information across the range of read lengths. The returned data frame has the option of being tidy, and if the 'tidy' parameter is set to TRUE, a position column will be added. Finally, if the 'alias' parameter is set to TRUE, the alias transcript name must have been provided at the generation of the ribo object, and the function will accept this aliased name in the 'transcript' parameter.

Ribo to generate the necessary ribo.object parameter

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

#get the experiments of interest that also contain coverage data
experiments <- c("Hela_1", "Hela_2", "Hela_3", "WT_1")

#the ribo file contains a transcript named 'MYC'
coverage.data <- get_coverage(ribo.object = sample,
                              name = "MYC",
                              range.lower = 2,
                              range.upper = 5,
                              length = TRUE,
                              experiment = experiments)