get_region_coordinates {ribor} | R Documentation

## Retrieves the region stop and start coordinates

### Description

The function `get_region_coordinates` retrieves the start and site positions for the UTR5, UTR5 Junction, CDS, UTR3 Junction, and UTR3 regions of every transcript.

### Usage

    get_region_coordinates(ribo.object, alias = FALSE)

### Arguments

`ribo.object` | A 'Ribo' object
`alias` | Option to return the transcript names as aliases

### Details

To note, because of the R-specific 1-based indexing, the positions start at 1 instead of 0 in other programming languages. The positions provided in the returned data.frame will correspond to the positions in the output of `get_coverage`.

Additionally, within the transcripts, there are edge cases. NA values found in the returned data.frame means that the region has no start and stop position and a length of zero after computing the boundaries of the UTR5 and UTR3 junction.

### Value

A data.frame of start and stop coordinates for every region

### Examples

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

    # get the region coordinates
    coord <- get_region_coordinates(sample, alias = TRUE)

[Package ribor version 0.99.8 Index]