get_region_coordinates: Retrieves the region stop and start coordinates
In ribosomeprofiling/ribor: An R Interface for Ribo Files
Description
Usage
Arguments
Details
Value
View source: R/annotation_functions.R
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
1
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
ribosomeprofiling/ribor documentation built on May 21, 2021, 8:02 a.m.
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Description Usage Arguments Details Value
View source: R/annotation_functions.R
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
1 | 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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