transcriptExtract: Extracting transcript information from the annotation file

In FcircSEC: Full Length Circular RNA Sequence Extraction and Classification

Description

This function extracts transcript information from the annotation file corresponding to reference genome

Usage

transcriptExtract(annotationFile, databaseName, outputfile)

Arguments

annotationFile	The annotation file (in gtf, gff or gff3 fromat) corresponding to the reference genome
databaseName	The database name from where the annotation file was downloaded (the possible options are "ncbi", "ucsc" and "other")
outputfile	The name of the output file

Value

The transcript information from the annotation file will be written in the output file 'outputfile'

Examples

#Loading an example annotation file and write to a file
#Here temporary directory is created as input-output
#directory. Please provide your own directory instead.
out_dir<-tempdir()
annotation_file<-data(refGenchr1)  
annotation_file<-refGenchr1
write.table(annotation_file, file.path(out_dir,"annotation_file.gtf"), 
         row.names=FALSE, sep="\t",quote=FALSE, col.names=FALSE)

#Extraction of transcript information. Here, the output will be generated in file 
#transcriptdata.txt in out_dir directory
transcriptExtract(file.path(out_dir,"annotation_file.gtf"), "ucsc", 
    file.path(out_dir, "transcriptdata.txt"))

FcircSEC documentation built on Jan. 31, 2020, 5:07 p.m.