get_internal_region_coordinates: Retrieves the region stop and start coordinates

In ribosomeprofiling/ribor: An R Interface for Ribo Files

Description

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

Usage

get_internal_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_internal_region_coordinates(sample, alias = TRUE)

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