get_region_coordinates {ribor} | R Documentation |
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.
get_region_coordinates(ribo.object, alias = FALSE)
ribo.object |
A 'Ribo' object |
alias |
Option to return the transcript names as aliases |
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.
A data.frame of start and stop coordinates for every region
# 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)