uorf.structure: Output gene structure information for uORFs.

In hsinyenwu/RiboPlotR: Plot Periodicity of Ribosome Profiling Data

Output gene structure information for uORFs.

Description

uORFs are not usually in the regular annotation files. Therefore you would need to create a gtf or gff of the uORFs of interest. This function takes a gtf or gff file to output several GRangesLists for the range information for transcripts, CDS and untranslation regions (UTRs) of the uORFs to the global environment. These GRangesLists will be used for other functions of RiboPlotter to define the features of the uORF

Usage

uorf.structure(uorf_annotation, format = "gtf", dataSource = "", organism = "")

Arguments

uorf_annotation	Path to the uORF annotation file in either gtf or gff format.
format	Is the uORF annotation file in gtf or gff format?
dataSource	Which organization annotate the genome? For example, TAIR or Araport for Arabidopsis.
organism	Which organism is it? For example, Arabidopsis.

Value

Multiple GRangesLists for uORFs with transcript, CDS and UTR information.

Examples

## Not run: 
uorf.structure(annotation="PathToArabidopsis.gff",format="gff",dataSource="Araport",organism="Arabidopsis thaliana")

## End(Not run)

hsinyenwu/RiboPlotR documentation built on Sept. 15, 2023, 12:29 a.m.