gene.structure: Output gene structure information.

In hsinyenwu/RiboPlotR: Plot Periodicity of Ribosome Profiling Data

Output gene structure information.

Description

Take a gtf or gff file to output several GRangesLists for the range information for transcripts, CDS and untranslation regions (UTRs) of the gene of interest to the global environment. These GRangesLists will be used for other functions of RiboPlotter to define the features of genes.

Usage

gene.structure(annotation, format = "gtf", dataSource = "", organism = "")

Arguments

annotation	Path to the annotation file in either gtf or gff format.
format	Is the 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 with transcript, CDS and UTR information.

Examples

## Not run: 
gene.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.